Starting phenix.real_space_refine on Tue Mar 26 07:25:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdv_3489/03_2024/5mdv_3489_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4638 5.49 5 Mg 440 5.21 5 S 172 5.16 5 C 75642 2.51 5 N 27820 2.21 5 O 41178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 ARG 3": "NH1" <-> "NH2" Residue "7 GLU 16": "OE1" <-> "OE2" Residue "7 ARG 17": "NH1" <-> "NH2" Residue "7 GLU 36": "OE1" <-> "OE2" Residue "7 GLU 40": "OE1" <-> "OE2" Residue "7 GLU 59": "OE1" <-> "OE2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "7 GLU 93": "OE1" <-> "OE2" Residue "7 GLU 102": "OE1" <-> "OE2" Residue "7 GLU 108": "OE1" <-> "OE2" Residue "7 GLU 122": "OE1" <-> "OE2" Residue "7 GLU 149": "OE1" <-> "OE2" Residue "7 ARG 154": "NH1" <-> "NH2" Residue "7 ARG 159": "NH1" <-> "NH2" Residue "7 GLU 167": "OE1" <-> "OE2" Residue "7 GLU 168": "OE1" <-> "OE2" Residue "7 ARG 200": "NH1" <-> "NH2" Residue "7 ARG 212": "NH1" <-> "NH2" Residue "7 GLU 233": "OE1" <-> "OE2" Residue "7 ARG 240": "NH1" <-> "NH2" Residue "7 GLU 299": "OE1" <-> "OE2" Residue "7 GLU 306": "OE1" <-> "OE2" Residue "7 GLU 311": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 55": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 4": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U GLU 101": "OE1" <-> "OE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W GLU 85": "OE1" <-> "OE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X GLU 43": "OE1" <-> "OE2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z GLU 37": "OE1" <-> "OE2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "Z GLU 59": "OE1" <-> "OE2" Residue "a GLU 11": "OE1" <-> "OE2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g GLU 44": "OE1" <-> "OE2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g GLU 118": "OE1" <-> "OE2" Residue "g GLU 133": "OE1" <-> "OE2" Residue "g GLU 169": "OE1" <-> "OE2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h GLU 28": "OE1" <-> "OE2" Residue "h GLU 46": "OE1" <-> "OE2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h GLU 110": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h GLU 161": "OE1" <-> "OE2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h GLU 166": "OE1" <-> "OE2" Residue "h GLU 188": "OE1" <-> "OE2" Residue "h GLU 206": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i GLU 147": "OE1" <-> "OE2" Residue "i GLU 160": "OE1" <-> "OE2" Residue "i GLU 166": "OE1" <-> "OE2" Residue "i GLU 172": "OE1" <-> "OE2" Residue "i GLU 202": "OE1" <-> "OE2" Residue "j GLU 10": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 55": "OE1" <-> "OE2" Residue "j GLU 65": "OE1" <-> "OE2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j GLU 101": "OE1" <-> "OE2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "j GLU 151": "OE1" <-> "OE2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k GLU 5": "OE1" <-> "OE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k GLU 65": "OE1" <-> "OE2" Residue "k GLU 69": "OE1" <-> "OE2" Residue "k GLU 73": "OE1" <-> "OE2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l GLU 21": "OE1" <-> "OE2" Residue "l GLU 40": "OE1" <-> "OE2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l GLU 58": "OE1" <-> "OE2" Residue "l GLU 63": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l GLU 123": "OE1" <-> "OE2" Residue "l GLU 146": "OE1" <-> "OE2" Residue "m GLU 42": "OE1" <-> "OE2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "m GLU 52": "OE1" <-> "OE2" Residue "m GLU 73": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 124": "OE1" <-> "OE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n GLU 36": "OE1" <-> "OE2" Residue "n TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o GLU 24": "OE1" <-> "OE2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o GLU 81": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p GLU 76": "OE1" <-> "OE2" Residue "p GLU 83": "OE1" <-> "OE2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 56": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q GLU 76": "OE1" <-> "OE2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r GLU 47": "OE1" <-> "OE2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s GLU 26": "OE1" <-> "OE2" Residue "s GLU 39": "OE1" <-> "OE2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "s GLU 92": "OE1" <-> "OE2" Residue "t GLU 6": "OE1" <-> "OE2" Residue "t ARG 17": "NH1" <-> "NH2" Residue "t GLU 26": "OE1" <-> "OE2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u GLU 34": "OE1" <-> "OE2" Residue "u GLU 45": "OE1" <-> "OE2" Residue "u GLU 47": "OE1" <-> "OE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v GLU 26": "OE1" <-> "OE2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v GLU 52": "OE1" <-> "OE2" Residue "v GLU 63": "OE1" <-> "OE2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w GLU 16": "OE1" <-> "OE2" Residue "w GLU 35": "OE1" <-> "OE2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x GLU 20": "OE1" <-> "OE2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "x GLU 65": "OE1" <-> "OE2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z GLU 8": "OE1" <-> "OE2" Residue "z GLU 24": "OE1" <-> "OE2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z GLU 39": "OE1" <-> "OE2" Residue "z GLU 44": "OE1" <-> "OE2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z GLU 63": "OE1" <-> "OE2" Residue "z ARG 66": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149892 Number of models: 1 Model: "" Number of chains: 67 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 288, 'rna2p_pyr': 163, 'rna3p': 16, 'rna3p_pur': 1379, 'rna3p_pyr': 1051} Link IDs: {'rna2p': 456, 'rna3p': 2446} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 119, 'rna2p_pyr': 88, 'rna3p': 10, 'rna3p_pur': 750, 'rna3p_pyr': 565} Link IDs: {'rna2p': 207, 'rna3p': 1326} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "5" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Unusual residues: {'8AN': 1} Classifications: {'RNA': 75, 'undetermined': 1} Modifications used: {'rna2p': 2, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'p': 1, 'rna2p': 13, 'rna3p': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2863 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 354} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1, 'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1191 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 296 Unusual residues: {' MG': 296} Classifications: {'undetermined': 296} Link IDs: {None: 295} Chain: "2" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Unusual residues: {' MG': 129} Classifications: {'undetermined': 129} Link IDs: {None: 128} Chain: "3" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "5" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 14 Unusual residues: {' MG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0LKL SG CYS a 16 127.837 197.279 41.950 1.00123.40 S ATOM A0LKX SG CYS a 18 129.823 197.349 41.476 1.00132.24 S ATOM A0NAH SG CYS f 11 182.271 134.595 116.365 1.00 79.27 S ATOM A0NB6 SG CYS f 14 180.591 131.591 116.192 1.00 50.41 S ATOM A0NE1 SG CYS f 27 182.681 132.127 118.872 1.00 57.81 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13146 " occ=0.50 Time building chain proxies: 59.30, per 1000 atoms: 0.40 Number of scatterers: 149892 At special positions: 0 Unit cell: (243.36, 287.04, 272.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 172 16.00 P 4638 15.00 Mg 440 11.99 O 41178 8.00 N 27820 7.00 C 75642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 69.35 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " Number of angles added : 3 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11734 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 201 helices and 77 sheets defined 41.1% alpha, 18.7% beta 1547 base pairs and 2346 stacking pairs defined. Time for finding SS restraints: 83.50 Creating SS restraints... Processing helix chain '6' and resid 14 through 23 removed outlier: 3.719A pdb=" N ASP 6 22 " --> pdb=" O ALA 6 18 " (cutoff:3.500A) Proline residue: 6 23 - end of helix Processing helix chain '7' and resid 4 through 26 removed outlier: 3.652A pdb=" N GLU 7 16 " --> pdb=" O GLN 7 12 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 44 Proline residue: 7 44 - end of helix Processing helix chain '7' and resid 45 through 50 removed outlier: 4.439A pdb=" N GLU 7 49 " --> pdb=" O ASP 7 45 " (cutoff:3.500A) Proline residue: 7 50 - end of helix No H-bonds generated for 'chain '7' and resid 45 through 50' Processing helix chain '7' and resid 51 through 88 removed outlier: 3.850A pdb=" N SER 7 62 " --> pdb=" O LYS 7 58 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU 7 63 " --> pdb=" O GLU 7 59 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU 7 78 " --> pdb=" O LYS 7 74 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU 7 86 " --> pdb=" O GLY 7 82 " (cutoff:3.500A) Processing helix chain '7' and resid 92 through 119 Processing helix chain '7' and resid 138 through 160 Processing helix chain '7' and resid 187 through 193 Processing helix chain '7' and resid 235 through 240 removed outlier: 3.561A pdb=" N LEU 7 239 " --> pdb=" O ASN 7 235 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARG 7 240 " --> pdb=" O PRO 7 236 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 235 through 240' Processing helix chain '7' and resid 251 through 257 Processing helix chain '7' and resid 279 through 318 removed outlier: 3.649A pdb=" N ILE 7 317 " --> pdb=" O ASN 7 313 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY 7 318 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) Processing helix chain '7' and resid 344 through 351 Processing helix chain '7' and resid 353 through 364 removed outlier: 3.738A pdb=" N ALA 7 359 " --> pdb=" O GLN 7 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 17 removed outlier: 7.415A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.559A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.739A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.837A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.817A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.885A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 97 through 103 removed outlier: 4.784A pdb=" N PHE C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 5.221A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 6.411A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 4.020A pdb=" N ALA D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.644A pdb=" N PHE D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N HIS D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 5.543A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.510A pdb=" N VAL E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 46 removed outlier: 4.711A pdb=" N ILE E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 46' Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.563A pdb=" N ASP E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 112 removed outlier: 4.765A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix removed outlier: 5.804A pdb=" N ARG E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.684A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.722A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.173A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 4.210A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.292A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 50 removed outlier: 4.031A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 73 removed outlier: 4.086A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'H' and resid 3 through 22 removed outlier: 3.679A pdb=" N ASP H 7 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA H 22 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 Processing helix chain 'H' and resid 62 through 70 Proline residue: H 68 - end of helix Processing helix chain 'H' and resid 73 through 79 removed outlier: 4.639A pdb=" N VAL H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Proline residue: H 79 - end of helix No H-bonds generated for 'chain 'H' and resid 73 through 79' Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.991A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.735A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.191A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 3.706A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 113 removed outlier: 3.792A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.775A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.126A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.822A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.398A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.108A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 120 removed outlier: 3.524A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.843A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.011A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.837A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.139A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 58 removed outlier: 4.099A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.240A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.443A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.390A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.137A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.523A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.618A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.663A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.947A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 73 removed outlier: 3.703A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.506A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.011A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.691A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.024A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.577A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.572A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.540A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.689A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 9 removed outlier: 4.135A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.595A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.694A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 44 through 51 removed outlier: 5.437A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 65 removed outlier: 3.802A pdb=" N ARG a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.601A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 31 Proline residue: c 31 - end of helix Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.819A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.030A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 54 through 63 Proline residue: e 63 - end of helix Processing helix chain 'e' and resid 26 through 31 removed outlier: 4.555A pdb=" N LEU e 29 " --> pdb=" O HIS e 26 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG e 30 " --> pdb=" O ALA e 27 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N HIS e 31 " --> pdb=" O ASN e 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 26 through 31' Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 24 through 32 removed outlier: 4.206A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix removed outlier: 5.689A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 24 through 32' Processing helix chain 'g' and resid 43 through 64 Proline residue: g 48 - end of helix removed outlier: 3.579A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 4.655A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 4.205A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.836A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 Processing helix chain 'h' and resid 72 through 78 removed outlier: 3.807A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.353A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.556A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.308A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.597A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.011A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.364A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.807A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.550A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 3.707A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER i 205 " --> pdb=" O VAL i 201 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 4.250A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 3.745A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 removed outlier: 3.631A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 19 removed outlier: 3.721A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix No H-bonds generated for 'chain 'k' and resid 11 through 19' Processing helix chain 'k' and resid 20 through 33 removed outlier: 3.884A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 3.540A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.586A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.550A pdb=" N ALA l 61 " --> pdb=" O SER l 57 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE l 62 " --> pdb=" O GLU l 58 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.671A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 153 removed outlier: 3.602A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA l 150 " --> pdb=" O GLU l 146 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE l 151 " --> pdb=" O ALA l 147 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA l 152 " --> pdb=" O ASN l 148 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS l 153 " --> pdb=" O LYS l 149 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 Proline residue: n 51 - end of helix removed outlier: 3.606A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 Processing helix chain 'n' and resid 94 through 102 Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.891A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 4.105A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.072A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.809A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 76 removed outlier: 4.930A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 104 removed outlier: 3.917A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.635A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.681A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.196A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 Processing helix chain 's' and resid 22 through 33 Processing helix chain 's' and resid 37 through 52 Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 44 removed outlier: 3.974A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.588A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 Processing helix chain 'w' and resid 11 through 17 removed outlier: 3.863A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.575A pdb=" N LEU w 29 " --> pdb=" O ASP w 25 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.679A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.465A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 41 removed outlier: 3.536A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.700A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.561A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '7' and resid 161 through 166 removed outlier: 6.666A pdb=" N THR 7 180 " --> pdb=" O ILE 7 166 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS 7 177 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASP 7 127 " --> pdb=" O GLU 7 225 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE 7 217 " --> pdb=" O GLY 7 135 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG 7 324 " --> pdb=" O VAL 7 198 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL 7 340 " --> pdb=" O ASP 7 335 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '7' and resid 241 through 244 removed outlier: 3.884A pdb=" N ILE 7 270 " --> pdb=" O HIS 7 265 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '7' and resid 167 through 170 Processing sheet with id= 4, first strand: chain 'B' and resid 75 through 78 removed outlier: 4.490A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 80 through 83 removed outlier: 5.356A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 162 through 165 removed outlier: 6.579A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 3 through 7 removed outlier: 6.401A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.575A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.642A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 1 through 6 removed outlier: 3.948A pdb=" N MET D 1 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 44 through 47 removed outlier: 6.513A pdb=" N ARG D 44 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALA D 87 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 117 through 120 Processing sheet with id= 13, first strand: chain 'E' and resid 65 through 69 removed outlier: 5.863A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 15, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 16, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.797A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 18, first strand: chain 'G' and resid 1 through 5 removed outlier: 4.882A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.369A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU G 114 " --> pdb=" O GLN G 133 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 23 through 28 removed outlier: 4.117A pdb=" N LEU H 23 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA H 25 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 55 through 60 removed outlier: 4.371A pdb=" N VAL I 69 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR I 59 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR I 67 " --> pdb=" O THR I 59 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 15 through 18 Processing sheet with id= 23, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.524A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 5 through 9 removed outlier: 4.186A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.129A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.681A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 30 through 36 removed outlier: 8.077A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.855A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.663A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER O 91 " --> pdb=" O THR O 24 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.540A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER P 85 " --> pdb=" O GLU P 27 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.513A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.503A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.438A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 36, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 37, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.177A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.802A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.950A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.326A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 40 through 45 removed outlier: 5.397A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 82 through 87 removed outlier: 7.077A pdb=" N ARG U 82 " --> pdb=" O LYS U 97 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 2 through 5 Processing sheet with id= 44, first strand: chain 'V' and resid 37 through 42 removed outlier: 3.612A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.257A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 47, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.553A pdb=" N SER X 19 " --> pdb=" O ASN X 23 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'X' and resid 35 through 41 removed outlier: 3.550A pdb=" N ARG X 45 " --> pdb=" O VAL X 40 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.211A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'a' and resid 20 through 25 removed outlier: 5.003A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.197A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 20 through 25 removed outlier: 6.962A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.642A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= 55, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.227A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 67 through 71 removed outlier: 3.588A pdb=" N ALA g 185 " --> pdb=" O PHE g 198 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 53 through 59 removed outlier: 3.506A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.622A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 141 through 145 removed outlier: 3.756A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.871A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 83 through 88 removed outlier: 7.249A pdb=" N HIS j 83 " --> pdb=" O PRO j 98 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 33 through 41 removed outlier: 6.492A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'k' and resid 38 through 42 removed outlier: 5.708A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL k 64 " --> pdb=" O TYR k 4 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL k 7 " --> pdb=" O MET k 88 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'k' and resid 43 through 47 removed outlier: 6.938A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 73 through 79 removed outlier: 6.382A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.187A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.548A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'n' and resid 5 through 11 removed outlier: 4.133A pdb=" N LYS n 27 " --> pdb=" O LEU n 61 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'o' and resid 37 through 42 removed outlier: 3.917A pdb=" N GLY o 38 " --> pdb=" O ASP o 75 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP o 75 " --> pdb=" O GLY o 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU o 42 " --> pdb=" O LEU o 71 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 71, first strand: chain 'p' and resid 42 through 45 removed outlier: 3.714A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL p 84 " --> pdb=" O THR p 108 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.149A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.181A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'u' and resid 4 through 10 removed outlier: 3.911A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.919A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 76 Processing sheet with id= 77, first strand: chain 'x' and resid 30 through 34 removed outlier: 5.047A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 2238 hydrogen bonds defined for protein. 6612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3892 hydrogen bonds 6158 hydrogen bond angles 0 basepair planarities 1547 basepair parallelities 2346 stacking parallelities Total time for adding SS restraints: 313.66 Time building geometry restraints manager: 74.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12589 1.30 - 1.43: 68676 1.43 - 1.56: 71204 1.56 - 1.70: 9294 1.70 - 1.83: 305 Bond restraints: 162068 Sorted by residual: bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.444 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" C4 5MU 5 54 " pdb=" C5 5MU 5 54 " ideal model delta sigma weight residual 1.802 1.447 0.355 2.00e-02 2.50e+03 3.16e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.463 0.339 2.00e-02 2.50e+03 2.88e+02 bond pdb=" N1 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.635 1.325 0.310 2.00e-02 2.50e+03 2.41e+02 bond pdb=" N1 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.635 1.378 0.257 2.00e-02 2.50e+03 1.65e+02 ... (remaining 162063 not shown) Histogram of bond angle deviations from ideal: 89.75 - 99.58: 56 99.58 - 109.41: 64669 109.41 - 119.24: 99419 119.24 - 129.08: 73326 129.08 - 138.91: 4285 Bond angle restraints: 241755 Sorted by residual: angle pdb=" O2' G7M 12069 " pdb=" C2' G7M 12069 " pdb=" C1' G7M 12069 " ideal model delta sigma weight residual 108.40 128.89 -20.49 1.50e+00 4.44e-01 1.87e+02 angle pdb=" C 0TD q 89 " pdb=" N LEU q 90 " pdb=" CA LEU q 90 " ideal model delta sigma weight residual 121.70 98.89 22.81 1.80e+00 3.09e-01 1.61e+02 angle pdb=" C3* PSU 2 516 " pdb=" C2* PSU 2 516 " pdb=" O2* PSU 2 516 " ideal model delta sigma weight residual 110.70 129.52 -18.82 1.50e+00 4.44e-01 1.57e+02 angle pdb=" O3' 2MA 12503 " pdb=" C3' 2MA 12503 " pdb=" C2' 2MA 12503 " ideal model delta sigma weight residual 109.50 127.36 -17.86 1.50e+00 4.44e-01 1.42e+02 angle pdb=" C3* PSU 5 55 " pdb=" C2* PSU 5 55 " pdb=" O2* PSU 5 55 " ideal model delta sigma weight residual 110.70 128.40 -17.70 1.50e+00 4.44e-01 1.39e+02 ... (remaining 241750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 90887 35.93 - 71.86: 11366 71.86 - 107.79: 1259 107.79 - 143.72: 21 143.72 - 179.65: 38 Dihedral angle restraints: 103571 sinusoidal: 85382 harmonic: 18189 Sorted by residual: dihedral pdb=" C5' A 1 404 " pdb=" C4' A 1 404 " pdb=" C3' A 1 404 " pdb=" O3' A 1 404 " ideal model delta sinusoidal sigma weight residual 147.00 75.81 71.19 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C5' U 5 17 " pdb=" C4' U 5 17 " pdb=" C3' U 5 17 " pdb=" O3' U 5 17 " ideal model delta sinusoidal sigma weight residual 147.00 77.97 69.03 1 8.00e+00 1.56e-02 9.63e+01 dihedral pdb=" C5' A 12602 " pdb=" C4' A 12602 " pdb=" C3' A 12602 " pdb=" O3' A 12602 " ideal model delta sinusoidal sigma weight residual 147.00 81.05 65.95 1 8.00e+00 1.56e-02 8.89e+01 ... (remaining 103568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 30603 0.338 - 0.677: 57 0.677 - 1.015: 12 1.015 - 1.354: 4 1.354 - 1.692: 9 Chirality restraints: 30685 Sorted by residual: chirality pdb=" C3' 2MA 12503 " pdb=" C4' 2MA 12503 " pdb=" O3' 2MA 12503 " pdb=" C2' 2MA 12503 " both_signs ideal model delta sigma weight residual False -2.74 -1.05 -1.69 2.00e-01 2.50e+01 7.16e+01 chirality pdb=" C2* PSU 5 55 " pdb=" C3* PSU 5 55 " pdb=" O2* PSU 5 55 " pdb=" C1* PSU 5 55 " both_signs ideal model delta sigma weight residual False -2.75 -1.14 -1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" C2* PSU 1 746 " pdb=" C3* PSU 1 746 " pdb=" O2* PSU 1 746 " pdb=" C1* PSU 1 746 " both_signs ideal model delta sigma weight residual False -2.52 -0.93 -1.59 2.00e-01 2.50e+01 6.33e+01 ... (remaining 30682 not shown) Planarity restraints: 13434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.008 2.00e-02 2.50e+03 6.31e-01 8.97e+03 pdb=" C4' 2MG 21207 " -0.466 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " -0.710 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " 0.625 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " 0.652 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " 0.192 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " -1.032 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " -0.217 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " 0.949 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " 0.030 2.00e-02 2.50e+03 6.26e-01 8.82e+03 pdb=" C4' 7MG 2 527 " 0.461 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.547 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " -0.599 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -0.717 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " -0.129 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 1.113 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.212 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -0.918 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' H2U 5 20 " -1.077 2.00e-02 2.50e+03 6.13e-01 8.47e+03 pdb=" C4' H2U 5 20 " 0.139 2.00e-02 2.50e+03 pdb=" O4' H2U 5 20 " 0.644 2.00e-02 2.50e+03 pdb=" C3' H2U 5 20 " -0.000 2.00e-02 2.50e+03 pdb=" O3' H2U 5 20 " 0.811 2.00e-02 2.50e+03 pdb=" C2' H2U 5 20 " -0.402 2.00e-02 2.50e+03 pdb=" O2' H2U 5 20 " -0.806 2.00e-02 2.50e+03 pdb=" C1' H2U 5 20 " 0.551 2.00e-02 2.50e+03 pdb=" N1 H2U 5 20 " 0.141 2.00e-02 2.50e+03 ... (remaining 13431 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 37 1.99 - 2.71: 13742 2.71 - 3.44: 196787 3.44 - 4.17: 511922 4.17 - 4.90: 681010 Nonbonded interactions: 1403498 Sorted by model distance: nonbonded pdb=" O4 U 2 961 " pdb=" N1 A 2 974 " model vdw 1.257 2.496 nonbonded pdb=" N1 A 12013 " pdb=" O4 U 12613 " model vdw 1.481 2.496 nonbonded pdb=" O4 U 2 37 " pdb=" N1 A 2 397 " model vdw 1.569 2.496 nonbonded pdb=" N1 A 12287 " pdb=" O4 U 12344 " model vdw 1.697 2.496 nonbonded pdb=" O4 U 1 234 " pdb=" N1 A 1 429 " model vdw 1.751 2.496 ... (remaining 1403493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 18.680 Check model and map are aligned: 1.660 Set scattering table: 1.040 Process input model: 668.750 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 710.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.358 162068 Z= 0.507 Angle : 1.262 28.557 241755 Z= 0.854 Chirality : 0.103 1.692 30685 Planarity : 0.020 0.631 13434 Dihedral : 23.696 179.646 91837 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.87 % Favored : 94.74 % Rotamer: Outliers : 7.74 % Allowed : 9.97 % Favored : 82.29 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.09), residues: 6269 helix: 0.16 (0.08), residues: 2225 sheet: -2.26 (0.13), residues: 1165 loop : -1.73 (0.10), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 248 HIS 0.011 0.002 HIS 6 21 PHE 0.052 0.003 PHE Q 106 TYR 0.035 0.003 TYR i 76 ARG 0.026 0.002 ARG b 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 1227 time to evaluate : 6.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 33 LYS cc_start: 0.9162 (mptp) cc_final: 0.8924 (mmtt) REVERT: 6 40 MET cc_start: 0.8309 (ptp) cc_final: 0.8047 (mtt) REVERT: 7 60 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.4282 (ptm-80) REVERT: 7 117 ARG cc_start: 0.7308 (tpt170) cc_final: 0.7092 (tpt170) REVERT: 7 129 TYR cc_start: 0.8119 (m-80) cc_final: 0.7804 (m-80) REVERT: 7 167 GLU cc_start: 0.8208 (tp30) cc_final: 0.7786 (tp30) REVERT: 7 170 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7648 (mm-30) REVERT: 7 172 GLU cc_start: 0.7225 (tt0) cc_final: 0.6990 (tp30) REVERT: 7 182 LYS cc_start: 0.7409 (tttt) cc_final: 0.7009 (tttm) REVERT: 7 234 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6513 (tp) REVERT: 7 256 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7972 (ptm160) REVERT: 7 292 LYS cc_start: 0.7651 (ttmp) cc_final: 0.7305 (ttpm) REVERT: 7 297 GLU cc_start: 0.7041 (tp30) cc_final: 0.6666 (tm-30) REVERT: 7 310 MET cc_start: 0.7028 (mmp) cc_final: 0.6149 (tpt) REVERT: 7 343 ARG cc_start: 0.7524 (mtp-110) cc_final: 0.7300 (mtp-110) REVERT: 7 352 SER cc_start: 0.8691 (t) cc_final: 0.8473 (t) REVERT: B 13 ARG cc_start: 0.8725 (tpt170) cc_final: 0.8502 (tpt170) REVERT: B 97 LYS cc_start: 0.8356 (mptt) cc_final: 0.7930 (ttpp) REVERT: B 100 GLU cc_start: 0.8500 (tt0) cc_final: 0.8191 (tt0) REVERT: B 125 LYS cc_start: 0.8371 (ptmm) cc_final: 0.7956 (pttm) REVERT: B 132 MET cc_start: 0.8897 (mtm) cc_final: 0.8545 (mtm) REVERT: B 161 TYR cc_start: 0.9170 (p90) cc_final: 0.8725 (p90) REVERT: B 177 ARG cc_start: 0.9256 (tpt90) cc_final: 0.9036 (mmm-85) REVERT: B 188 CYS cc_start: 0.8971 (m) cc_final: 0.8590 (m) REVERT: B 242 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8603 (mptt) REVERT: B 270 ARG cc_start: 0.8259 (mmm160) cc_final: 0.7197 (ttt-90) REVERT: C 7 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8289 (ttpp) REVERT: C 13 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8936 (ptm160) REVERT: C 22 ILE cc_start: 0.8882 (mt) cc_final: 0.8648 (mp) REVERT: C 40 LEU cc_start: 0.8531 (mt) cc_final: 0.8329 (mm) REVERT: C 105 LYS cc_start: 0.8459 (mttt) cc_final: 0.8026 (mmtt) REVERT: C 149 ASN cc_start: 0.9241 (t0) cc_final: 0.9002 (t0) REVERT: C 165 MET cc_start: 0.8635 (ttt) cc_final: 0.8322 (ttt) REVERT: C 177 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8560 (t) REVERT: D 16 GLU cc_start: 0.7905 (tt0) cc_final: 0.7680 (tp30) REVERT: D 93 SER cc_start: 0.8927 (t) cc_final: 0.8593 (p) REVERT: D 140 ASP cc_start: 0.7475 (m-30) cc_final: 0.7150 (t0) REVERT: D 155 GLU cc_start: 0.7627 (tp30) cc_final: 0.7190 (mp0) REVERT: D 163 ASN cc_start: 0.9163 (t0) cc_final: 0.8795 (t160) REVERT: D 184 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: E 3 LYS cc_start: 0.8084 (tttt) cc_final: 0.7821 (tttt) REVERT: E 32 GLU cc_start: 0.8244 (tt0) cc_final: 0.7979 (tt0) REVERT: E 38 MET cc_start: 0.8293 (mtt) cc_final: 0.8033 (mtt) REVERT: E 96 MET cc_start: 0.8724 (ttp) cc_final: 0.8429 (ttp) REVERT: E 98 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: E 105 THR cc_start: 0.8770 (m) cc_final: 0.8510 (p) REVERT: E 120 LYS cc_start: 0.8721 (mttt) cc_final: 0.8399 (ptmt) REVERT: E 125 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7937 (mtp-110) REVERT: E 134 GLU cc_start: 0.8316 (tt0) cc_final: 0.7910 (mt-10) REVERT: E 142 ASP cc_start: 0.6684 (t70) cc_final: 0.6268 (t0) REVERT: F 27 LYS cc_start: 0.6746 (mttt) cc_final: 0.6154 (mppt) REVERT: F 112 PRO cc_start: 0.8156 (Cg_endo) cc_final: 0.7937 (Cg_exo) REVERT: F 153 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8422 (ttp80) REVERT: F 176 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6089 (ptpt) REVERT: G 8 LYS cc_start: 0.8439 (tttp) cc_final: 0.8154 (ttmm) REVERT: G 11 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7049 (m110) REVERT: G 35 LYS cc_start: 0.7688 (mttt) cc_final: 0.7442 (mttp) REVERT: G 53 GLU cc_start: 0.6361 (mp0) cc_final: 0.5948 (pm20) REVERT: G 127 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4930 (mm-30) REVERT: H 38 MET cc_start: 0.2431 (mtm) cc_final: 0.2156 (mmm) REVERT: J 13 ARG cc_start: 0.8558 (mtt90) cc_final: 0.8231 (mtt90) REVERT: J 57 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8796 (pp) REVERT: J 98 GLU cc_start: 0.8755 (mp0) cc_final: 0.8519 (mp0) REVERT: J 129 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: K 17 ARG cc_start: 0.8205 (mpp-170) cc_final: 0.7955 (mtt180) REVERT: K 54 LYS cc_start: 0.8778 (tttt) cc_final: 0.8525 (ttpt) REVERT: K 73 ASP cc_start: 0.8424 (p0) cc_final: 0.8189 (p0) REVERT: K 93 GLN cc_start: 0.8450 (pt0) cc_final: 0.7773 (mm110) REVERT: K 98 ARG cc_start: 0.8256 (ttt-90) cc_final: 0.8009 (ttt180) REVERT: K 111 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8050 (ttpt) REVERT: K 113 MET cc_start: 0.8273 (tpt) cc_final: 0.7907 (mmm) REVERT: L 1 MET cc_start: 0.7784 (ttp) cc_final: 0.7522 (ttp) REVERT: L 84 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7991 (mtpt) REVERT: L 129 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8214 (ptpp) REVERT: M 60 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: M 75 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8201 (mt-10) REVERT: M 103 TYR cc_start: 0.9088 (m-80) cc_final: 0.8709 (m-80) REVERT: M 127 LYS cc_start: 0.8260 (ttmp) cc_final: 0.7960 (tptm) REVERT: M 135 VAL cc_start: 0.8269 (t) cc_final: 0.7894 (m) REVERT: N 32 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7905 (mt-10) REVERT: N 69 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8271 (mmt90) REVERT: N 106 ASP cc_start: 0.8879 (p0) cc_final: 0.8516 (p0) REVERT: O 13 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8237 (ttt90) REVERT: O 16 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7391 (mmt90) REVERT: O 46 GLU cc_start: 0.8150 (pt0) cc_final: 0.7913 (tt0) REVERT: P 83 SER cc_start: 0.8873 (t) cc_final: 0.8629 (p) REVERT: P 88 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7789 (ttt-90) REVERT: P 89 ARG cc_start: 0.8109 (ptt90) cc_final: 0.7480 (ptp-110) REVERT: P 110 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7988 (pt) REVERT: P 114 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7312 (mm) REVERT: R 19 THR cc_start: 0.8862 (m) cc_final: 0.8591 (t) REVERT: R 29 THR cc_start: 0.8380 (p) cc_final: 0.8047 (m) REVERT: R 31 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7552 (mm-30) REVERT: R 40 MET cc_start: 0.9161 (ttt) cc_final: 0.8934 (ttt) REVERT: R 70 GLU cc_start: 0.8574 (tt0) cc_final: 0.8277 (tp30) REVERT: R 97 LYS cc_start: 0.8473 (tttp) cc_final: 0.8264 (tttm) REVERT: S 38 TYR cc_start: 0.9040 (m-80) cc_final: 0.8621 (m-80) REVERT: S 41 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8963 (mmmt) REVERT: S 73 LYS cc_start: 0.8534 (mttt) cc_final: 0.8173 (mtpp) REVERT: S 78 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7951 (mm-30) REVERT: T 9 LYS cc_start: 0.8234 (mttt) cc_final: 0.7890 (mmtp) REVERT: T 33 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7809 (tttm) REVERT: T 49 LYS cc_start: 0.8024 (tttt) cc_final: 0.7757 (tptp) REVERT: V 34 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8101 (ptpt) REVERT: V 43 ASP cc_start: 0.8336 (t0) cc_final: 0.8121 (t70) REVERT: V 46 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8399 (mtpt) REVERT: W 70 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: W 81 SER cc_start: 0.9119 (p) cc_final: 0.8875 (p) REVERT: W 83 GLU cc_start: 0.8219 (pt0) cc_final: 0.7928 (pt0) REVERT: Z 8 THR cc_start: 0.8837 (m) cc_final: 0.8587 (m) REVERT: Z 56 LYS cc_start: 0.8190 (pttt) cc_final: 0.7838 (tttm) REVERT: Z 58 GLU cc_start: 0.7232 (tt0) cc_final: 0.6973 (tt0) REVERT: b 36 GLU cc_start: 0.8799 (pt0) cc_final: 0.8535 (pt0) REVERT: c 33 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7345 (mtpt) REVERT: c 36 LEU cc_start: 0.8966 (mt) cc_final: 0.8743 (mt) REVERT: c 44 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8176 (mtp180) REVERT: d 14 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8599 (mtt180) REVERT: e 30 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.7396 (tpm170) REVERT: e 52 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8016 (tttm) REVERT: g 7 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.6801 (tmt-80) REVERT: g 28 LYS cc_start: 0.7285 (tttt) cc_final: 0.6796 (ttpp) REVERT: g 37 LYS cc_start: 0.7088 (tptt) cc_final: 0.6737 (mppt) REVERT: g 59 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6367 (mtmt) REVERT: g 105 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7886 (ptmt) REVERT: g 199 VAL cc_start: 0.8564 (p) cc_final: 0.8290 (t) REVERT: g 203 ASN cc_start: 0.7763 (t0) cc_final: 0.7158 (t0) REVERT: h 27 LYS cc_start: 0.8370 (ttmt) cc_final: 0.7399 (mptt) REVERT: h 82 GLU cc_start: 0.7907 (tp30) cc_final: 0.7493 (mp0) REVERT: h 85 GLU cc_start: 0.7514 (tp30) cc_final: 0.7083 (tp30) REVERT: h 88 ARG cc_start: 0.6928 (ttp80) cc_final: 0.6410 (ttp80) REVERT: h 89 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7017 (pttm) REVERT: h 110 GLU cc_start: 0.7639 (mp0) cc_final: 0.7360 (mp0) REVERT: h 118 ASP cc_start: 0.7472 (m-30) cc_final: 0.7022 (m-30) REVERT: h 166 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7937 (mt-10) REVERT: h 208 LEU cc_start: 0.7446 (mt) cc_final: 0.6872 (mm) REVERT: i 45 LYS cc_start: 0.7818 (mttm) cc_final: 0.7415 (mtpt) REVERT: i 124 MET cc_start: 0.8257 (mtt) cc_final: 0.7935 (mmm) REVERT: i 128 ARG cc_start: 0.8004 (mtp180) cc_final: 0.6900 (mtm180) REVERT: i 138 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8175 (m) REVERT: i 172 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7143 (pp20) REVERT: i 178 MET cc_start: 0.7924 (mtt) cc_final: 0.7720 (mtt) REVERT: i 187 GLU cc_start: 0.8032 (tt0) cc_final: 0.7795 (mm-30) REVERT: i 192 SER cc_start: 0.8675 (t) cc_final: 0.8447 (t) REVERT: j 45 ARG cc_start: 0.8242 (mtp85) cc_final: 0.8038 (mmm-85) REVERT: j 60 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7914 (mt) REVERT: j 72 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8346 (mt) REVERT: j 115 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8365 (mt) REVERT: k 7 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8582 (t) REVERT: k 36 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8490 (mp) REVERT: k 38 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8407 (ptt180) REVERT: k 41 ASP cc_start: 0.8356 (t0) cc_final: 0.8142 (m-30) REVERT: k 53 LYS cc_start: 0.8946 (mttt) cc_final: 0.8732 (mttp) REVERT: k 93 LYS cc_start: 0.8212 (mtpt) cc_final: 0.8012 (mmtm) REVERT: l 40 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: l 74 GLU cc_start: 0.8132 (pt0) cc_final: 0.7366 (tp30) REVERT: l 79 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5289 (tpt90) REVERT: l 130 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8173 (t0) REVERT: l 144 MET cc_start: 0.7176 (ttt) cc_final: 0.6953 (ttt) REVERT: m 27 MET cc_start: 0.9197 (ptp) cc_final: 0.8766 (pmm) REVERT: m 31 LYS cc_start: 0.8296 (ttpm) cc_final: 0.7857 (ptmm) REVERT: m 50 LYS cc_start: 0.7975 (tttp) cc_final: 0.7435 (tptm) REVERT: m 58 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8163 (tt0) REVERT: m 96 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8530 (ttm) REVERT: m 117 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7600 (mtm-85) REVERT: n 33 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7453 (mtm180) REVERT: n 42 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7416 (mm-30) REVERT: n 124 ARG cc_start: 0.8869 (ttm-80) cc_final: 0.8506 (mtm-85) REVERT: o 7 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6382 (ttp-170) REVERT: o 27 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: p 13 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6497 (tpp-160) REVERT: p 85 MET cc_start: 0.8029 (mtt) cc_final: 0.7687 (mmp) REVERT: q 5 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8441 (m110) REVERT: q 9 ARG cc_start: 0.8160 (ttp-110) cc_final: 0.7848 (ttm110) REVERT: q 10 LYS cc_start: 0.8292 (tttt) cc_final: 0.8077 (tttm) REVERT: q 25 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8408 (mm-30) REVERT: q 56 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7735 (ttm110) REVERT: q 76 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8077 (mt-10) REVERT: q 108 LYS cc_start: 0.8586 (mttt) cc_final: 0.8052 (mmpt) REVERT: r 77 ILE cc_start: 0.8382 (mt) cc_final: 0.8180 (mp) REVERT: r 93 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7726 (mmp80) REVERT: t 22 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8240 (p) REVERT: t 67 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8432 (mt) REVERT: t 80 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7263 (tm130) REVERT: v 60 GLU cc_start: 0.7572 (tt0) cc_final: 0.6831 (tm-30) REVERT: v 76 VAL cc_start: 0.8545 (m) cc_final: 0.8315 (m) REVERT: x 21 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6678 (mtmt) REVERT: x 32 ARG cc_start: 0.8068 (ptt180) cc_final: 0.7785 (mtm110) REVERT: y 48 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7287 (tp40) REVERT: y 49 LYS cc_start: 0.8032 (tppt) cc_final: 0.7697 (ttmm) REVERT: y 52 ASN cc_start: 0.8174 (m-40) cc_final: 0.7616 (m110) REVERT: y 57 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8474 (mp) REVERT: y 64 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7605 (mptp) REVERT: y 85 LYS cc_start: 0.7751 (tttt) cc_final: 0.7240 (mmtp) REVERT: z 33 ARG cc_start: 0.7920 (tmt170) cc_final: 0.7434 (ttm170) REVERT: z 55 ARG cc_start: 0.7659 (mtm-85) cc_final: 0.6734 (mmt180) REVERT: z 59 LYS cc_start: 0.6679 (ttmm) cc_final: 0.6467 (tppt) outliers start: 404 outliers final: 101 residues processed: 1518 average time/residue: 2.3185 time to fit residues: 4977.0451 Evaluate side-chains 1138 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 984 time to evaluate : 6.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 42 GLU Chi-restraints excluded: chain 7 residue 60 ARG Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 337 ARG Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain a residue 40 CYS Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain c residue 50 LYS Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 59 LYS Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 96 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain p residue 13 ARG Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 48 GLN Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 64 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 907 optimal weight: 0.9990 chunk 814 optimal weight: 5.9990 chunk 452 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 549 optimal weight: 5.9990 chunk 435 optimal weight: 10.0000 chunk 842 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 512 optimal weight: 3.9990 chunk 627 optimal weight: 2.9990 chunk 976 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 6 HIS 6 14 ASN 6 32 ASN 7 72 GLN 7 280 GLN B 21 ASN B 163 GLN C 32 ASN C 150 GLN D 24 ASN D 41 GLN D 46 GLN E 23 ASN F 116 GLN N 9 GLN N 18 GLN O 100 HIS Q 20 GLN Q 71 GLN S 9 HIS S 40 ASN a 20 ASN g 39 HIS g 42 ASN g 120 GLN g 177 ASN g 178 ASN h 102 ASN i 116 GLN l 52 GLN o 64 GLN p 22 HIS p 28 ASN s 66 GLN u 18 GLN x 52 HIS y 3 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 162068 Z= 0.363 Angle : 0.733 16.693 241755 Z= 0.391 Chirality : 0.043 0.365 30685 Planarity : 0.007 0.143 13434 Dihedral : 23.465 179.940 79657 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 6.84 % Allowed : 17.58 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.10), residues: 6269 helix: 2.51 (0.11), residues: 2269 sheet: -1.77 (0.13), residues: 1191 loop : -1.23 (0.10), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 248 HIS 0.010 0.001 HIS w 74 PHE 0.021 0.002 PHE Q 57 TYR 0.018 0.002 TYR D 35 ARG 0.015 0.001 ARG q 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 1135 time to evaluate : 6.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 33 LYS cc_start: 0.9215 (mptp) cc_final: 0.8914 (mmtm) REVERT: 6 40 MET cc_start: 0.8340 (ptp) cc_final: 0.8054 (mtt) REVERT: 7 70 LEU cc_start: 0.5524 (mt) cc_final: 0.5118 (mm) REVERT: 7 129 TYR cc_start: 0.8186 (m-80) cc_final: 0.7831 (m-80) REVERT: 7 157 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6700 (tp30) REVERT: 7 166 ILE cc_start: 0.8230 (mt) cc_final: 0.7932 (mm) REVERT: 7 169 SER cc_start: 0.7730 (m) cc_final: 0.7519 (t) REVERT: 7 172 GLU cc_start: 0.7483 (tt0) cc_final: 0.7020 (tp30) REVERT: 7 182 LYS cc_start: 0.7320 (tttt) cc_final: 0.6966 (mtpt) REVERT: 7 234 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.6441 (tp) REVERT: 7 255 ASN cc_start: 0.7998 (m-40) cc_final: 0.7575 (m-40) REVERT: 7 256 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8013 (ptm160) REVERT: 7 285 ASP cc_start: 0.7731 (m-30) cc_final: 0.7395 (m-30) REVERT: 7 292 LYS cc_start: 0.7682 (ttmp) cc_final: 0.7069 (tmtm) REVERT: 7 297 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: 7 299 GLU cc_start: 0.7230 (tt0) cc_final: 0.7027 (tt0) REVERT: 7 303 LYS cc_start: 0.6887 (mttm) cc_final: 0.6580 (mptt) REVERT: 7 310 MET cc_start: 0.7319 (mmp) cc_final: 0.6581 (mmm) REVERT: 7 314 LYS cc_start: 0.7712 (mttt) cc_final: 0.7485 (mttt) REVERT: 7 352 SER cc_start: 0.8665 (t) cc_final: 0.8460 (t) REVERT: B 97 LYS cc_start: 0.8403 (mptt) cc_final: 0.7951 (ttpp) REVERT: B 114 ASP cc_start: 0.8192 (m-30) cc_final: 0.7888 (m-30) REVERT: B 125 LYS cc_start: 0.8344 (ptmm) cc_final: 0.7866 (pttp) REVERT: B 133 ARG cc_start: 0.8331 (ptp-110) cc_final: 0.8037 (ptp90) REVERT: B 161 TYR cc_start: 0.9119 (p90) cc_final: 0.8737 (p90) REVERT: B 188 CYS cc_start: 0.8928 (m) cc_final: 0.8628 (m) REVERT: B 242 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8543 (mptt) REVERT: B 270 ARG cc_start: 0.8122 (mmm160) cc_final: 0.6911 (ttt-90) REVERT: C 1 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6599 (tmm) REVERT: C 7 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8258 (ttpp) REVERT: C 13 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8864 (ptm160) REVERT: C 40 LEU cc_start: 0.8589 (mt) cc_final: 0.8339 (mm) REVERT: C 86 GLU cc_start: 0.6708 (pp20) cc_final: 0.6468 (pp20) REVERT: C 105 LYS cc_start: 0.8344 (mttt) cc_final: 0.7975 (mmtt) REVERT: C 165 MET cc_start: 0.8761 (ttt) cc_final: 0.8403 (ttt) REVERT: C 184 ARG cc_start: 0.8417 (mtt180) cc_final: 0.8167 (mpp80) REVERT: D 16 GLU cc_start: 0.8021 (tt0) cc_final: 0.7766 (tp30) REVERT: D 40 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7961 (ttp-170) REVERT: D 69 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7294 (ptp-170) REVERT: D 122 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: D 132 LYS cc_start: 0.7777 (tttm) cc_final: 0.7382 (ttpt) REVERT: D 141 MET cc_start: 0.6928 (mmt) cc_final: 0.6485 (mmt) REVERT: D 150 THR cc_start: 0.8336 (m) cc_final: 0.8018 (p) REVERT: D 155 GLU cc_start: 0.7559 (tp30) cc_final: 0.7183 (mp0) REVERT: D 184 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8003 (t0) REVERT: D 197 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7259 (tp30) REVERT: E 17 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7985 (mtp) REVERT: E 120 LYS cc_start: 0.8761 (mttt) cc_final: 0.8297 (ptmt) REVERT: E 133 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7672 (mtt-85) REVERT: E 142 ASP cc_start: 0.6644 (t70) cc_final: 0.6275 (t0) REVERT: E 165 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7468 (mt-10) REVERT: F 27 LYS cc_start: 0.7028 (mttt) cc_final: 0.6320 (mppt) REVERT: F 95 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8124 (ptt90) REVERT: F 99 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7352 (mtpt) REVERT: F 112 PRO cc_start: 0.7975 (Cg_endo) cc_final: 0.7674 (Cg_exo) REVERT: F 153 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8139 (ttp80) REVERT: F 176 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5524 (ptpt) REVERT: G 8 LYS cc_start: 0.8460 (tttp) cc_final: 0.8171 (ttmm) REVERT: G 11 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7480 (m110) REVERT: G 35 LYS cc_start: 0.7809 (mttt) cc_final: 0.7576 (mttp) REVERT: G 53 GLU cc_start: 0.6256 (mp0) cc_final: 0.5617 (pm20) REVERT: G 114 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6542 (mm-30) REVERT: G 117 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5290 (mt) REVERT: G 127 GLU cc_start: 0.5557 (pt0) cc_final: 0.5285 (mp0) REVERT: H 38 MET cc_start: 0.2091 (mtm) cc_final: 0.1760 (mmm) REVERT: H 86 MET cc_start: 0.2923 (mmm) cc_final: 0.1581 (ttp) REVERT: I 11 GLN cc_start: 0.3166 (OUTLIER) cc_final: 0.1497 (tm-30) REVERT: I 116 MET cc_start: 0.1297 (mmp) cc_final: 0.0488 (ptp) REVERT: J 61 LYS cc_start: 0.8598 (mttp) cc_final: 0.8381 (mtmt) REVERT: J 98 GLU cc_start: 0.8790 (mp0) cc_final: 0.8377 (mp0) REVERT: J 129 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: K 17 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7788 (mtp180) REVERT: K 93 GLN cc_start: 0.8495 (pt0) cc_final: 0.7711 (mm110) REVERT: K 111 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8035 (ttpt) REVERT: K 113 MET cc_start: 0.8001 (tpt) cc_final: 0.7712 (mmm) REVERT: K 114 LYS cc_start: 0.8254 (tttt) cc_final: 0.7730 (mmpt) REVERT: L 1 MET cc_start: 0.8188 (ttp) cc_final: 0.7898 (ttp) REVERT: L 84 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7956 (mtpt) REVERT: M 54 THR cc_start: 0.8360 (m) cc_final: 0.8078 (m) REVERT: M 75 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8153 (mt-10) REVERT: M 127 LYS cc_start: 0.8325 (ttmp) cc_final: 0.7946 (tttm) REVERT: N 32 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8183 (mm-30) REVERT: N 69 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8603 (mmt90) REVERT: O 13 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8081 (ttt90) REVERT: O 16 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7464 (mmt90) REVERT: O 46 GLU cc_start: 0.8236 (pt0) cc_final: 0.8026 (tt0) REVERT: O 80 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7625 (mt-10) REVERT: P 29 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8296 (mtmm) REVERT: P 83 SER cc_start: 0.8604 (t) cc_final: 0.8299 (p) REVERT: P 114 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7063 (mm) REVERT: R 16 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7387 (mt-10) REVERT: R 19 THR cc_start: 0.8920 (m) cc_final: 0.8530 (t) REVERT: R 29 THR cc_start: 0.8338 (p) cc_final: 0.7899 (m) REVERT: R 31 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7674 (mm-30) REVERT: R 48 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7652 (pttm) REVERT: R 70 GLU cc_start: 0.8534 (tt0) cc_final: 0.8267 (tp30) REVERT: R 86 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: S 22 ASP cc_start: 0.8178 (m-30) cc_final: 0.7952 (m-30) REVERT: S 38 TYR cc_start: 0.8908 (m-80) cc_final: 0.8448 (m-80) REVERT: S 73 LYS cc_start: 0.8440 (mttt) cc_final: 0.8091 (mtpt) REVERT: T 9 LYS cc_start: 0.7991 (mttt) cc_final: 0.7787 (mmtp) REVERT: T 33 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7795 (tttp) REVERT: T 49 LYS cc_start: 0.8046 (tttt) cc_final: 0.7731 (tptp) REVERT: U 29 LEU cc_start: 0.8214 (mt) cc_final: 0.7964 (mm) REVERT: V 7 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: V 12 GLN cc_start: 0.8582 (mt0) cc_final: 0.8316 (mt0) REVERT: V 43 ASP cc_start: 0.8371 (t0) cc_final: 0.8080 (t70) REVERT: W 68 LYS cc_start: 0.8844 (tptp) cc_final: 0.8170 (tppt) REVERT: W 70 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: Y 2 LYS cc_start: 0.6939 (mtpt) cc_final: 0.6733 (tttt) REVERT: Y 23 ARG cc_start: 0.8246 (mtm180) cc_final: 0.7752 (mtt90) REVERT: Y 59 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6872 (mm-30) REVERT: Z 56 LYS cc_start: 0.8266 (pttt) cc_final: 0.7844 (pttp) REVERT: Z 58 GLU cc_start: 0.7225 (tt0) cc_final: 0.6963 (tt0) REVERT: b 40 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6942 (mmp-170) REVERT: c 8 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8111 (mtpt) REVERT: c 33 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7395 (mtpt) REVERT: c 36 LEU cc_start: 0.8864 (mt) cc_final: 0.8660 (mt) REVERT: c 47 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8296 (m) REVERT: g 28 LYS cc_start: 0.7174 (tttt) cc_final: 0.6711 (ttpp) REVERT: g 37 LYS cc_start: 0.6952 (tptt) cc_final: 0.6547 (mppt) REVERT: g 95 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7982 (ttp-110) REVERT: g 105 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7539 (pttm) REVERT: g 203 ASN cc_start: 0.7800 (t0) cc_final: 0.7171 (t0) REVERT: h 27 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7443 (mptt) REVERT: h 46 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7856 (mm-30) REVERT: h 82 GLU cc_start: 0.7179 (tp30) cc_final: 0.6977 (tm-30) REVERT: h 85 GLU cc_start: 0.7415 (tp30) cc_final: 0.7185 (mm-30) REVERT: h 89 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7263 (ptpp) REVERT: h 110 GLU cc_start: 0.7667 (mp0) cc_final: 0.7439 (mp0) REVERT: h 121 THR cc_start: 0.8819 (m) cc_final: 0.8218 (m) REVERT: h 187 SER cc_start: 0.9044 (t) cc_final: 0.8676 (t) REVERT: h 193 TYR cc_start: 0.8406 (m-80) cc_final: 0.8118 (m-10) REVERT: h 200 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8647 (t) REVERT: i 45 LYS cc_start: 0.7806 (mttm) cc_final: 0.7491 (mtpm) REVERT: i 70 ARG cc_start: 0.8684 (tpp80) cc_final: 0.7580 (ttp-110) REVERT: i 128 ARG cc_start: 0.7862 (mtp180) cc_final: 0.6767 (mtm180) REVERT: i 142 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8524 (t) REVERT: i 172 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7364 (tm-30) REVERT: i 187 GLU cc_start: 0.8095 (tt0) cc_final: 0.7621 (mm-30) REVERT: j 26 LYS cc_start: 0.9130 (ttpm) cc_final: 0.8869 (ttmm) REVERT: j 41 ASP cc_start: 0.8235 (p0) cc_final: 0.7907 (p0) REVERT: j 45 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7710 (mmm-85) REVERT: j 60 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8060 (mt) REVERT: j 61 GLN cc_start: 0.8139 (tt0) cc_final: 0.7902 (mm110) REVERT: j 115 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8433 (mt) REVERT: j 130 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8913 (p) REVERT: k 5 GLU cc_start: 0.8072 (tt0) cc_final: 0.7831 (tt0) REVERT: k 7 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8710 (t) REVERT: k 23 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8333 (tm-30) REVERT: l 40 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: l 42 ILE cc_start: 0.8647 (mt) cc_final: 0.8299 (mp) REVERT: l 48 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: l 52 GLN cc_start: 0.7416 (mm110) cc_final: 0.7208 (mp10) REVERT: l 79 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.5620 (tpt90) REVERT: l 129 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7494 (mm-30) REVERT: l 130 ASN cc_start: 0.8124 (t0) cc_final: 0.7912 (t0) REVERT: l 144 MET cc_start: 0.7230 (ttt) cc_final: 0.6939 (ttt) REVERT: l 148 ASN cc_start: 0.8436 (m-40) cc_final: 0.8170 (m-40) REVERT: m 27 MET cc_start: 0.9270 (ptp) cc_final: 0.8823 (ptp) REVERT: m 31 LYS cc_start: 0.8529 (ttpm) cc_final: 0.8037 (ptmm) REVERT: m 50 LYS cc_start: 0.8150 (tttp) cc_final: 0.7580 (tptm) REVERT: m 58 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8069 (tt0) REVERT: m 74 SER cc_start: 0.8623 (t) cc_final: 0.8396 (m) REVERT: n 33 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7260 (mtm180) REVERT: n 42 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7465 (mm-30) REVERT: n 61 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7182 (pp) REVERT: n 123 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8596 (tpt-90) REVERT: n 124 ARG cc_start: 0.8778 (ttm-80) cc_final: 0.8438 (mtm-85) REVERT: o 60 ASP cc_start: 0.8697 (m-30) cc_final: 0.8307 (m-30) REVERT: p 69 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7481 (mmt-90) REVERT: q 5 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8428 (m110) REVERT: q 9 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7874 (ttm110) REVERT: q 10 LYS cc_start: 0.8300 (tttt) cc_final: 0.8054 (tttm) REVERT: q 25 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8229 (mm-30) REVERT: q 76 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7890 (tt0) REVERT: q 108 LYS cc_start: 0.8568 (mttt) cc_final: 0.8072 (mmpt) REVERT: r 76 SER cc_start: 0.8083 (m) cc_final: 0.7742 (p) REVERT: r 93 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7881 (mmp80) REVERT: r 104 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8005 (p) REVERT: s 40 ASP cc_start: 0.7748 (m-30) cc_final: 0.7477 (t0) REVERT: s 46 LEU cc_start: 0.8230 (mt) cc_final: 0.7936 (mm) REVERT: s 49 GLN cc_start: 0.8230 (mt0) cc_final: 0.7969 (mt0) REVERT: t 67 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8642 (mt) REVERT: t 80 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7010 (tm130) REVERT: u 42 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8495 (mp) REVERT: u 47 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: v 60 GLU cc_start: 0.7528 (tt0) cc_final: 0.6913 (tm-30) REVERT: v 76 VAL cc_start: 0.8552 (m) cc_final: 0.8156 (m) REVERT: w 48 ARG cc_start: 0.7916 (mtm110) cc_final: 0.6856 (mmt90) REVERT: x 17 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7605 (mmpt) REVERT: x 21 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6839 (mtmt) REVERT: x 32 ARG cc_start: 0.8234 (ptt180) cc_final: 0.7846 (mtm110) REVERT: y 48 GLN cc_start: 0.8150 (mm110) cc_final: 0.7867 (tp40) REVERT: y 49 LYS cc_start: 0.8103 (tppt) cc_final: 0.7713 (ttmt) REVERT: y 57 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8244 (mp) REVERT: y 85 LYS cc_start: 0.7369 (tttt) cc_final: 0.6856 (mmmm) REVERT: z 33 ARG cc_start: 0.8023 (tmt170) cc_final: 0.7560 (ttm170) REVERT: z 55 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.6858 (mmt180) REVERT: z 59 LYS cc_start: 0.6913 (ttmm) cc_final: 0.6694 (tppt) outliers start: 357 outliers final: 149 residues processed: 1348 average time/residue: 2.2997 time to fit residues: 4402.7525 Evaluate side-chains 1254 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1049 time to evaluate : 6.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 42 GLU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 268 THR Chi-restraints excluded: chain 7 residue 297 GLU Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain 7 residue 360 SER Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 8 LYS Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 152 GLU Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain u residue 47 GLU Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 542 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 812 optimal weight: 9.9990 chunk 664 optimal weight: 0.9980 chunk 269 optimal weight: 6.9990 chunk 977 optimal weight: 7.9990 chunk 1056 optimal weight: 0.8980 chunk 870 optimal weight: 8.9990 chunk 969 optimal weight: 0.8980 chunk 333 optimal weight: 8.9990 chunk 784 optimal weight: 4.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 ASN E 63 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN K 29 HIS L 93 ASN N 18 GLN O 100 HIS Q 20 GLN Q 72 ASN Y 27 ASN Z 9 GLN g 42 ASN g 168 HIS g 178 ASN g 227 GLN h 102 ASN i 116 GLN i 140 ASN o 35 GLN p 28 ASN t 28 GLN u 18 GLN u 29 ASN u 63 GLN w 54 GLN w 74 HIS x 69 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 162068 Z= 0.261 Angle : 0.634 15.604 241755 Z= 0.343 Chirality : 0.038 0.378 30685 Planarity : 0.006 0.134 13434 Dihedral : 23.276 179.863 79527 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 6.54 % Allowed : 19.72 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 6269 helix: 2.51 (0.11), residues: 2269 sheet: -1.33 (0.14), residues: 1181 loop : -0.95 (0.11), residues: 2819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 248 HIS 0.005 0.001 HIS w 74 PHE 0.018 0.002 PHE G 91 TYR 0.022 0.002 TYR u 17 ARG 0.011 0.001 ARG M 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1067 time to evaluate : 6.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 31 LYS cc_start: 0.9213 (tttm) cc_final: 0.8871 (tmtm) REVERT: 6 33 LYS cc_start: 0.9117 (mptp) cc_final: 0.8845 (mmtm) REVERT: 6 40 MET cc_start: 0.8279 (ptp) cc_final: 0.7918 (mtt) REVERT: 7 157 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6725 (tp30) REVERT: 7 166 ILE cc_start: 0.8236 (mt) cc_final: 0.7900 (mm) REVERT: 7 169 SER cc_start: 0.7667 (m) cc_final: 0.7430 (t) REVERT: 7 172 GLU cc_start: 0.7492 (tt0) cc_final: 0.6994 (tp30) REVERT: 7 182 LYS cc_start: 0.7295 (tttt) cc_final: 0.6988 (mtpt) REVERT: 7 234 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.6237 (tp) REVERT: 7 255 ASN cc_start: 0.8087 (m-40) cc_final: 0.7784 (m-40) REVERT: 7 256 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8003 (ptm160) REVERT: 7 285 ASP cc_start: 0.7565 (m-30) cc_final: 0.7210 (m-30) REVERT: 7 292 LYS cc_start: 0.7746 (ttmp) cc_final: 0.7171 (tttm) REVERT: 7 297 GLU cc_start: 0.7161 (tp30) cc_final: 0.6743 (tm-30) REVERT: 7 299 GLU cc_start: 0.7208 (tt0) cc_final: 0.7000 (tt0) REVERT: 7 303 LYS cc_start: 0.6991 (mttm) cc_final: 0.6667 (mptt) REVERT: 7 310 MET cc_start: 0.7372 (mmp) cc_final: 0.6663 (mmm) REVERT: 7 352 SER cc_start: 0.8610 (t) cc_final: 0.8380 (t) REVERT: B 13 ARG cc_start: 0.8720 (tpt170) cc_final: 0.8504 (tpt170) REVERT: B 23 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7836 (mm-30) REVERT: B 97 LYS cc_start: 0.8403 (mptt) cc_final: 0.7878 (ttpp) REVERT: B 114 ASP cc_start: 0.8226 (m-30) cc_final: 0.7966 (m-30) REVERT: B 125 LYS cc_start: 0.8326 (ptmm) cc_final: 0.7777 (pttm) REVERT: B 161 TYR cc_start: 0.9073 (p90) cc_final: 0.8695 (p90) REVERT: B 188 CYS cc_start: 0.8885 (m) cc_final: 0.8543 (m) REVERT: B 270 ARG cc_start: 0.8042 (mmm160) cc_final: 0.6823 (ttt-90) REVERT: C 1 MET cc_start: 0.7181 (tmm) cc_final: 0.6966 (tmm) REVERT: C 7 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8285 (ttpp) REVERT: C 13 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8990 (ptm160) REVERT: C 30 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7869 (mp0) REVERT: C 105 LYS cc_start: 0.8456 (mttt) cc_final: 0.7984 (mmtt) REVERT: C 165 MET cc_start: 0.8753 (ttt) cc_final: 0.8419 (ttt) REVERT: D 16 GLU cc_start: 0.8031 (tt0) cc_final: 0.7808 (tp30) REVERT: D 69 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7096 (ptp-170) REVERT: D 122 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: D 132 LYS cc_start: 0.7609 (tttm) cc_final: 0.7253 (ttpt) REVERT: D 155 GLU cc_start: 0.7513 (tp30) cc_final: 0.7191 (mp0) REVERT: D 171 ASP cc_start: 0.8044 (t70) cc_final: 0.7662 (t70) REVERT: D 184 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7939 (t0) REVERT: D 191 ASP cc_start: 0.7759 (t70) cc_final: 0.7447 (t70) REVERT: D 197 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7395 (tp30) REVERT: E 120 LYS cc_start: 0.8687 (mttt) cc_final: 0.8273 (ptmt) REVERT: E 133 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7870 (mtt-85) REVERT: F 27 LYS cc_start: 0.7029 (mttt) cc_final: 0.6342 (mppt) REVERT: F 95 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7825 (ptm-80) REVERT: F 99 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7488 (mtpt) REVERT: F 176 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5427 (ptpt) REVERT: G 11 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7343 (m110) REVERT: G 35 LYS cc_start: 0.7761 (mttt) cc_final: 0.7514 (mttp) REVERT: G 42 LYS cc_start: 0.6794 (tptt) cc_final: 0.6432 (tptp) REVERT: G 66 ASN cc_start: 0.4317 (OUTLIER) cc_final: 0.4024 (p0) REVERT: G 114 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: G 117 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5189 (OUTLIER) REVERT: G 127 GLU cc_start: 0.5601 (pt0) cc_final: 0.5324 (mp0) REVERT: H 38 MET cc_start: 0.2408 (mtm) cc_final: 0.2075 (mmm) REVERT: I 11 GLN cc_start: 0.3230 (OUTLIER) cc_final: 0.1597 (tm-30) REVERT: J 98 GLU cc_start: 0.8760 (mp0) cc_final: 0.8311 (mp0) REVERT: J 129 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: K 17 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7759 (mtp180) REVERT: K 93 GLN cc_start: 0.8373 (pt0) cc_final: 0.7705 (mm110) REVERT: K 111 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8067 (ttpt) REVERT: K 113 MET cc_start: 0.7942 (tpt) cc_final: 0.7684 (mmm) REVERT: K 114 LYS cc_start: 0.8341 (tttt) cc_final: 0.7831 (mmpt) REVERT: M 20 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8401 (mt) REVERT: M 60 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: M 75 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8237 (mt-10) REVERT: M 127 LYS cc_start: 0.8349 (ttmp) cc_final: 0.8002 (tttm) REVERT: N 32 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8240 (mm-30) REVERT: N 69 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8640 (mmt90) REVERT: O 16 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7531 (mmt90) REVERT: O 80 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7601 (mt-10) REVERT: P 29 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8217 (mtmm) REVERT: P 83 SER cc_start: 0.8537 (t) cc_final: 0.8241 (p) REVERT: P 87 LYS cc_start: 0.8842 (mmtp) cc_final: 0.8459 (mmtm) REVERT: P 110 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8027 (mt) REVERT: Q 13 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7947 (mtp180) REVERT: R 11 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8705 (mt0) REVERT: R 13 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8287 (ttp80) REVERT: R 19 THR cc_start: 0.8903 (m) cc_final: 0.8486 (t) REVERT: R 24 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8413 (ttpp) REVERT: R 31 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7705 (mm-30) REVERT: R 70 GLU cc_start: 0.8499 (tt0) cc_final: 0.8264 (tp30) REVERT: R 86 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8626 (mt0) REVERT: S 38 TYR cc_start: 0.8902 (m-80) cc_final: 0.8544 (m-80) REVERT: S 73 LYS cc_start: 0.8490 (mttt) cc_final: 0.8125 (mtpp) REVERT: T 9 LYS cc_start: 0.8029 (mttt) cc_final: 0.7813 (mmtp) REVERT: T 33 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7798 (tttm) REVERT: T 49 LYS cc_start: 0.8161 (tttt) cc_final: 0.7942 (ttmm) REVERT: U 6 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7877 (mtt180) REVERT: U 29 LEU cc_start: 0.8274 (mt) cc_final: 0.8025 (mm) REVERT: V 7 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: V 43 ASP cc_start: 0.8247 (t0) cc_final: 0.7929 (t70) REVERT: W 68 LYS cc_start: 0.8673 (tptp) cc_final: 0.8160 (tppt) REVERT: W 70 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: X 72 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7809 (ttp-110) REVERT: Y 6 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7639 (mt) REVERT: Y 23 ARG cc_start: 0.8300 (mtm180) cc_final: 0.7721 (mtt90) REVERT: Z 56 LYS cc_start: 0.8209 (pttt) cc_final: 0.7790 (pttp) REVERT: Z 58 GLU cc_start: 0.7258 (tt0) cc_final: 0.6950 (tt0) REVERT: a 1 MET cc_start: 0.7876 (ptp) cc_final: 0.7631 (mtm) REVERT: c 33 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7374 (mtpt) REVERT: d 14 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8408 (mtt-85) REVERT: e 15 LYS cc_start: 0.8713 (mptt) cc_final: 0.8453 (mppt) REVERT: g 36 ASN cc_start: 0.7687 (t0) cc_final: 0.7376 (t0) REVERT: g 37 LYS cc_start: 0.7087 (tptt) cc_final: 0.6677 (mppt) REVERT: g 63 ARG cc_start: 0.7589 (ttp-110) cc_final: 0.7310 (mtp-110) REVERT: g 105 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7440 (tttm) REVERT: g 113 ARG cc_start: 0.7014 (tpt170) cc_final: 0.6725 (tpt-90) REVERT: g 137 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.5924 (tpp80) REVERT: g 146 ASN cc_start: 0.7203 (m-40) cc_final: 0.6078 (t0) REVERT: h 85 GLU cc_start: 0.7341 (tp30) cc_final: 0.7010 (mm-30) REVERT: h 89 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7322 (ptpp) REVERT: h 110 GLU cc_start: 0.7646 (mp0) cc_final: 0.7386 (mp0) REVERT: h 118 ASP cc_start: 0.7287 (m-30) cc_final: 0.6635 (m-30) REVERT: h 121 THR cc_start: 0.8905 (m) cc_final: 0.8493 (m) REVERT: h 147 LYS cc_start: 0.8833 (mmpt) cc_final: 0.8535 (tppt) REVERT: h 185 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8594 (t0) REVERT: h 187 SER cc_start: 0.9030 (t) cc_final: 0.8599 (t) REVERT: h 193 TYR cc_start: 0.8357 (m-80) cc_final: 0.8128 (m-10) REVERT: h 200 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8632 (t) REVERT: i 45 LYS cc_start: 0.7772 (mttm) cc_final: 0.7463 (mtpm) REVERT: i 60 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8505 (ttpt) REVERT: i 70 ARG cc_start: 0.8678 (tpp80) cc_final: 0.7579 (ttp-110) REVERT: i 128 ARG cc_start: 0.7955 (mtp180) cc_final: 0.6871 (mtm180) REVERT: i 142 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8502 (t) REVERT: i 172 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7361 (tm-30) REVERT: i 187 GLU cc_start: 0.8093 (tt0) cc_final: 0.7638 (mm-30) REVERT: j 26 LYS cc_start: 0.9076 (ttpm) cc_final: 0.8731 (ttmm) REVERT: j 45 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7724 (mmm-85) REVERT: j 61 GLN cc_start: 0.8164 (tt0) cc_final: 0.7896 (mm110) REVERT: j 94 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8429 (t) REVERT: j 115 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8364 (mt) REVERT: k 5 GLU cc_start: 0.8050 (tt0) cc_final: 0.7813 (tt0) REVERT: k 7 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8707 (t) REVERT: k 23 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8288 (tm-30) REVERT: k 86 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8219 (mtt-85) REVERT: l 21 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: l 31 MET cc_start: 0.8927 (ttm) cc_final: 0.8694 (ttm) REVERT: l 42 ILE cc_start: 0.8753 (mt) cc_final: 0.8388 (mp) REVERT: l 79 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5204 (tmt170) REVERT: l 129 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7472 (mm-30) REVERT: l 130 ASN cc_start: 0.8148 (t0) cc_final: 0.7928 (t0) REVERT: m 27 MET cc_start: 0.9266 (ptp) cc_final: 0.8872 (ptp) REVERT: m 31 LYS cc_start: 0.8525 (ttpm) cc_final: 0.8101 (ptmm) REVERT: m 50 LYS cc_start: 0.8110 (tttp) cc_final: 0.7533 (tptm) REVERT: m 51 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8082 (t) REVERT: m 58 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8127 (mt-10) REVERT: n 22 LYS cc_start: 0.7255 (tttt) cc_final: 0.7009 (ttmm) REVERT: n 33 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7337 (mtm180) REVERT: n 42 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7418 (mm-30) REVERT: n 61 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7356 (pt) REVERT: n 124 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8317 (mtm-85) REVERT: o 60 ASP cc_start: 0.8706 (m-30) cc_final: 0.8345 (m-30) REVERT: o 97 ASP cc_start: 0.7635 (t70) cc_final: 0.7417 (t0) REVERT: p 69 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7266 (mmm160) REVERT: p 76 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: q 9 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.7854 (ttm170) REVERT: q 25 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8209 (mm-30) REVERT: q 44 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8472 (tppp) REVERT: q 76 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7953 (tt0) REVERT: q 108 LYS cc_start: 0.8531 (mttt) cc_final: 0.8094 (mmtm) REVERT: r 29 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7216 (ttm170) REVERT: r 76 SER cc_start: 0.8035 (m) cc_final: 0.7684 (p) REVERT: r 93 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7691 (mmp80) REVERT: s 49 GLN cc_start: 0.8096 (mt0) cc_final: 0.7895 (mt0) REVERT: t 80 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7279 (tm130) REVERT: u 42 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8474 (mp) REVERT: v 75 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8054 (tt) REVERT: w 48 ARG cc_start: 0.7817 (mtm110) cc_final: 0.6945 (mmt90) REVERT: x 17 LYS cc_start: 0.7928 (mmmm) cc_final: 0.7517 (mmpt) REVERT: x 21 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6765 (mtmt) REVERT: x 32 ARG cc_start: 0.8184 (ptt180) cc_final: 0.7774 (ptp-170) REVERT: x 63 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7382 (p) REVERT: y 48 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: y 49 LYS cc_start: 0.8170 (tppt) cc_final: 0.7781 (ttmt) REVERT: y 85 LYS cc_start: 0.7273 (tttt) cc_final: 0.6821 (mmmm) REVERT: z 33 ARG cc_start: 0.7990 (tmt170) cc_final: 0.7527 (ttm170) REVERT: z 55 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.6921 (mmt180) REVERT: z 59 LYS cc_start: 0.7321 (ttmm) cc_final: 0.7100 (tppt) outliers start: 341 outliers final: 157 residues processed: 1267 average time/residue: 2.2563 time to fit residues: 4071.1715 Evaluate side-chains 1221 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1012 time to evaluate : 6.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain 7 residue 42 GLU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 240 ARG Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 268 THR Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain 7 residue 360 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 60 LYS Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 29 ARG Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 48 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 966 optimal weight: 5.9990 chunk 735 optimal weight: 0.6980 chunk 507 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 466 optimal weight: 20.0000 chunk 656 optimal weight: 7.9990 chunk 981 optimal weight: 10.0000 chunk 1039 optimal weight: 8.9990 chunk 512 optimal weight: 1.9990 chunk 930 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 72 GLN D 92 HIS E 23 ASN E 63 GLN F 22 GLN F 104 ASN F 128 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 93 ASN N 18 GLN P 115 ASN Q 20 GLN Q 72 ASN S 60 HIS T 70 HIS Y 27 ASN e 28 ASN h 102 ASN i 59 GLN i 116 GLN p 28 ASN q 112 GLN t 46 HIS w 74 HIS x 14 HIS x 43 ASN y 3 ASN y 84 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 162068 Z= 0.388 Angle : 0.702 15.958 241755 Z= 0.372 Chirality : 0.041 0.374 30685 Planarity : 0.007 0.140 13434 Dihedral : 23.267 179.104 79489 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 7.44 % Allowed : 20.22 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.10), residues: 6269 helix: 2.02 (0.11), residues: 2266 sheet: -1.12 (0.14), residues: 1196 loop : -0.88 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 248 HIS 0.011 0.001 HIS w 74 PHE 0.021 0.002 PHE j 33 TYR 0.017 0.002 TYR i 103 ARG 0.009 0.001 ARG M 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1049 time to evaluate : 6.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 33 LYS cc_start: 0.9257 (mptp) cc_final: 0.8918 (mmtm) REVERT: 7 157 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6735 (tp30) REVERT: 7 169 SER cc_start: 0.7582 (m) cc_final: 0.7379 (t) REVERT: 7 172 GLU cc_start: 0.7489 (tt0) cc_final: 0.6993 (tp30) REVERT: 7 182 LYS cc_start: 0.7367 (tttt) cc_final: 0.7021 (mtpt) REVERT: 7 200 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7196 (ttm-80) REVERT: 7 234 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6331 (tp) REVERT: 7 255 ASN cc_start: 0.8145 (m-40) cc_final: 0.7806 (m-40) REVERT: 7 256 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7998 (ptm160) REVERT: 7 292 LYS cc_start: 0.7754 (ttmp) cc_final: 0.7168 (tttm) REVERT: 7 297 GLU cc_start: 0.7218 (tp30) cc_final: 0.6783 (tm-30) REVERT: 7 303 LYS cc_start: 0.7000 (mttm) cc_final: 0.6631 (mptt) REVERT: 7 310 MET cc_start: 0.7434 (mmp) cc_final: 0.6529 (tpt) REVERT: 7 352 SER cc_start: 0.8606 (t) cc_final: 0.8331 (t) REVERT: B 97 LYS cc_start: 0.8380 (mptt) cc_final: 0.7798 (ttpt) REVERT: B 111 LYS cc_start: 0.8336 (pttt) cc_final: 0.7851 (ptpp) REVERT: B 161 TYR cc_start: 0.9108 (p90) cc_final: 0.8837 (p90) REVERT: B 188 CYS cc_start: 0.8868 (m) cc_final: 0.8459 (m) REVERT: B 251 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8751 (mm-40) REVERT: B 270 ARG cc_start: 0.8087 (mmm160) cc_final: 0.6900 (ttt-90) REVERT: C 1 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6801 (tmm) REVERT: C 7 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8287 (ttpp) REVERT: C 13 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9080 (ptm160) REVERT: C 28 GLU cc_start: 0.8368 (tt0) cc_final: 0.8097 (tt0) REVERT: C 105 LYS cc_start: 0.8484 (mttt) cc_final: 0.7990 (mmtt) REVERT: C 165 MET cc_start: 0.8796 (ttt) cc_final: 0.8463 (ttt) REVERT: C 184 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7690 (mtt-85) REVERT: D 16 GLU cc_start: 0.8033 (tt0) cc_final: 0.7796 (tp30) REVERT: D 40 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8233 (ttp-170) REVERT: D 69 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7189 (ptp-170) REVERT: D 122 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: D 132 LYS cc_start: 0.7641 (tttm) cc_final: 0.7288 (ttpt) REVERT: D 136 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7018 (tm130) REVERT: D 139 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7691 (tttp) REVERT: D 155 GLU cc_start: 0.7648 (tp30) cc_final: 0.7299 (mp0) REVERT: D 171 ASP cc_start: 0.8191 (t70) cc_final: 0.7826 (t70) REVERT: D 184 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7919 (t0) REVERT: E 120 LYS cc_start: 0.8762 (mttt) cc_final: 0.8310 (ptmm) REVERT: E 133 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7878 (mtt-85) REVERT: E 165 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7525 (mt-10) REVERT: F 27 LYS cc_start: 0.7021 (mttt) cc_final: 0.6410 (mppt) REVERT: F 95 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8178 (ptt90) REVERT: F 99 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7626 (mtmm) REVERT: F 176 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5325 (ptpt) REVERT: G 11 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7265 (m110) REVERT: G 35 LYS cc_start: 0.7713 (mttt) cc_final: 0.7460 (mttp) REVERT: G 42 LYS cc_start: 0.6546 (tptt) cc_final: 0.6297 (tptp) REVERT: G 66 ASN cc_start: 0.4212 (OUTLIER) cc_final: 0.3758 (p0) REVERT: G 114 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6678 (mm-30) REVERT: G 117 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5042 (OUTLIER) REVERT: G 127 GLU cc_start: 0.5520 (pt0) cc_final: 0.5295 (tp30) REVERT: H 38 MET cc_start: 0.2403 (mtm) cc_final: 0.2079 (mmm) REVERT: I 11 GLN cc_start: 0.3167 (OUTLIER) cc_final: 0.1589 (tm-30) REVERT: J 98 GLU cc_start: 0.8769 (mp0) cc_final: 0.8411 (mp0) REVERT: J 129 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: K 66 LYS cc_start: 0.9047 (tttt) cc_final: 0.8828 (mtpt) REVERT: K 93 GLN cc_start: 0.8359 (pt0) cc_final: 0.7632 (mm110) REVERT: K 111 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8106 (ttpt) REVERT: K 113 MET cc_start: 0.8043 (tpt) cc_final: 0.7762 (mmm) REVERT: K 114 LYS cc_start: 0.8373 (tttt) cc_final: 0.7870 (mmpt) REVERT: M 60 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: M 75 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8168 (mt-10) REVERT: M 91 TYR cc_start: 0.9315 (p90) cc_final: 0.9114 (p90) REVERT: M 103 TYR cc_start: 0.9105 (m-80) cc_final: 0.8639 (m-80) REVERT: M 104 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8567 (mt-10) REVERT: M 127 LYS cc_start: 0.8344 (ttmp) cc_final: 0.7937 (tttm) REVERT: N 32 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8233 (mm-30) REVERT: N 63 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8822 (mtp85) REVERT: N 69 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8666 (mmt90) REVERT: O 13 ARG cc_start: 0.8559 (tmm160) cc_final: 0.7980 (ttt90) REVERT: O 16 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7501 (mmt90) REVERT: O 80 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7573 (mt-10) REVERT: P 7 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: P 83 SER cc_start: 0.8551 (t) cc_final: 0.8246 (p) REVERT: Q 13 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8045 (mtp180) REVERT: R 19 THR cc_start: 0.8907 (m) cc_final: 0.8480 (t) REVERT: R 31 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7778 (mm-30) REVERT: R 70 GLU cc_start: 0.8491 (tt0) cc_final: 0.8229 (tp30) REVERT: R 86 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8618 (mt0) REVERT: S 38 TYR cc_start: 0.9025 (m-80) cc_final: 0.8499 (m-80) REVERT: S 73 LYS cc_start: 0.8503 (mttt) cc_final: 0.8086 (mtpp) REVERT: T 33 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7783 (tttm) REVERT: T 49 LYS cc_start: 0.8325 (tttt) cc_final: 0.8115 (tttp) REVERT: U 6 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7917 (mtt180) REVERT: U 47 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8078 (ttmm) REVERT: V 7 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: V 12 GLN cc_start: 0.8562 (mt0) cc_final: 0.8327 (mt0) REVERT: V 43 ASP cc_start: 0.8287 (t0) cc_final: 0.7964 (t70) REVERT: W 68 LYS cc_start: 0.8725 (tptp) cc_final: 0.8232 (tppt) REVERT: W 70 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: Y 6 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7719 (mt) REVERT: Y 23 ARG cc_start: 0.8359 (mtm180) cc_final: 0.7952 (mtt90) REVERT: Z 56 LYS cc_start: 0.8269 (pttt) cc_final: 0.7874 (pttp) REVERT: Z 58 GLU cc_start: 0.7275 (tt0) cc_final: 0.6987 (tt0) REVERT: b 40 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7098 (mmt180) REVERT: d 1 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7931 (mtp) REVERT: d 14 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8428 (mtt-85) REVERT: f 8 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8595 (mtpt) REVERT: g 36 ASN cc_start: 0.7602 (t0) cc_final: 0.7311 (t0) REVERT: g 37 LYS cc_start: 0.7151 (tptt) cc_final: 0.6739 (mppt) REVERT: g 63 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.7139 (mtp-110) REVERT: g 105 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7540 (tttm) REVERT: g 137 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.5970 (tpp80) REVERT: g 138 THR cc_start: 0.6840 (m) cc_final: 0.6505 (p) REVERT: g 146 ASN cc_start: 0.7239 (m-40) cc_final: 0.6216 (OUTLIER) REVERT: h 27 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7416 (mptt) REVERT: h 85 GLU cc_start: 0.7508 (tp30) cc_final: 0.7008 (mm-30) REVERT: h 89 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7402 (ptpp) REVERT: h 110 GLU cc_start: 0.7672 (mp0) cc_final: 0.7443 (mp0) REVERT: h 118 ASP cc_start: 0.7395 (m-30) cc_final: 0.6610 (m-30) REVERT: h 121 THR cc_start: 0.8899 (m) cc_final: 0.8332 (m) REVERT: h 147 LYS cc_start: 0.8846 (mmpt) cc_final: 0.8500 (mmmt) REVERT: h 187 SER cc_start: 0.8996 (t) cc_final: 0.8625 (t) REVERT: h 193 TYR cc_start: 0.8355 (m-80) cc_final: 0.8119 (m-10) REVERT: i 45 LYS cc_start: 0.7814 (mttm) cc_final: 0.7545 (mtpm) REVERT: i 60 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8698 (ttpt) REVERT: i 70 ARG cc_start: 0.8725 (tpp80) cc_final: 0.7637 (ttp-110) REVERT: i 128 ARG cc_start: 0.7917 (mtp180) cc_final: 0.6892 (mtm180) REVERT: i 172 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7357 (tm-30) REVERT: i 187 GLU cc_start: 0.8060 (tt0) cc_final: 0.7616 (mm-30) REVERT: j 26 LYS cc_start: 0.9095 (ttpm) cc_final: 0.8838 (ttmm) REVERT: j 45 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7910 (mmm-85) REVERT: j 94 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8570 (t) REVERT: j 115 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8305 (mt) REVERT: k 5 GLU cc_start: 0.8118 (tt0) cc_final: 0.7913 (tt0) REVERT: k 7 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8670 (t) REVERT: k 86 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7783 (mtt-85) REVERT: l 21 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: l 42 ILE cc_start: 0.8797 (mt) cc_final: 0.8424 (mp) REVERT: l 52 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: l 58 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: l 79 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.5367 (tmt170) REVERT: l 129 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7453 (mm-30) REVERT: l 130 ASN cc_start: 0.8138 (t0) cc_final: 0.7893 (t0) REVERT: l 144 MET cc_start: 0.7079 (ttt) cc_final: 0.6780 (ttt) REVERT: l 148 ASN cc_start: 0.8287 (m-40) cc_final: 0.8035 (m-40) REVERT: m 4 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8704 (mp10) REVERT: m 31 LYS cc_start: 0.8581 (ttpm) cc_final: 0.8154 (ptmm) REVERT: m 43 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: m 50 LYS cc_start: 0.8180 (tttp) cc_final: 0.7592 (tptm) REVERT: m 58 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8020 (tt0) REVERT: n 22 LYS cc_start: 0.7451 (tttt) cc_final: 0.7039 (mttm) REVERT: n 33 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7164 (mtm180) REVERT: n 42 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7424 (mm-30) REVERT: n 124 ARG cc_start: 0.8744 (ttm-80) cc_final: 0.8411 (mtm-85) REVERT: o 7 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6785 (mmm160) REVERT: o 37 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.5445 (mmm160) REVERT: o 60 ASP cc_start: 0.8695 (m-30) cc_final: 0.8430 (m-30) REVERT: o 97 ASP cc_start: 0.7679 (t70) cc_final: 0.7471 (t0) REVERT: p 18 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: p 69 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7250 (mmm160) REVERT: p 76 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: p 119 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7372 (t0) REVERT: q 9 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7849 (ttm110) REVERT: q 25 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8222 (mm-30) REVERT: q 44 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8406 (tppp) REVERT: q 76 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7947 (tt0) REVERT: q 108 LYS cc_start: 0.8568 (mttt) cc_final: 0.8129 (mmtm) REVERT: r 29 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7433 (mtt180) REVERT: r 76 SER cc_start: 0.8102 (m) cc_final: 0.7722 (p) REVERT: r 81 MET cc_start: 0.8263 (mtt) cc_final: 0.7737 (mtt) REVERT: r 93 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7857 (mmp80) REVERT: s 40 ASP cc_start: 0.7794 (m-30) cc_final: 0.7581 (m-30) REVERT: s 49 GLN cc_start: 0.8120 (mt0) cc_final: 0.7822 (mt0) REVERT: s 65 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7356 (mtt90) REVERT: t 80 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7249 (tm130) REVERT: u 42 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8475 (mp) REVERT: u 47 GLU cc_start: 0.7852 (pt0) cc_final: 0.7569 (pt0) REVERT: v 60 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: w 38 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8411 (mttt) REVERT: x 17 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7529 (mmpt) REVERT: x 21 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6742 (mtmt) REVERT: x 32 ARG cc_start: 0.8185 (ptt180) cc_final: 0.7766 (ptp-170) REVERT: x 63 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7607 (p) REVERT: y 48 GLN cc_start: 0.8083 (mm110) cc_final: 0.7721 (mm-40) REVERT: y 49 LYS cc_start: 0.8214 (tppt) cc_final: 0.7810 (ttmm) REVERT: y 85 LYS cc_start: 0.7377 (tttt) cc_final: 0.6942 (mmmm) REVERT: z 33 ARG cc_start: 0.8000 (tmt170) cc_final: 0.7519 (ttm170) REVERT: z 47 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7872 (mtm110) REVERT: z 55 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.6928 (mmt180) outliers start: 388 outliers final: 207 residues processed: 1274 average time/residue: 2.2505 time to fit residues: 4090.6064 Evaluate side-chains 1300 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1027 time to evaluate : 6.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 42 LYS Chi-restraints excluded: chain 7 residue 42 GLU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 240 ARG Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 268 THR Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 314 LYS Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain 7 residue 360 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 63 ARG Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 153 ASP Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 60 LYS Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 52 GLN Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 4 GLN Chi-restraints excluded: chain m residue 43 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 29 ARG Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 65 ARG Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 12 LYS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 38 LYS Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain z residue 47 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 865 optimal weight: 1.9990 chunk 589 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 773 optimal weight: 5.9990 chunk 428 optimal weight: 10.0000 chunk 886 optimal weight: 2.9990 chunk 718 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 530 optimal weight: 6.9990 chunk 932 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 304 ASN 7 313 ASN E 23 ASN E 63 GLN F 104 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 93 ASN L 104 GLN N 18 GLN Q 20 GLN Q 72 ASN Y 27 ASN e 28 ASN h 102 ASN k 11 HIS p 28 ASN p 119 ASN u 18 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 3 ASN y 84 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 162068 Z= 0.262 Angle : 0.632 15.809 241755 Z= 0.340 Chirality : 0.037 0.380 30685 Planarity : 0.006 0.133 13434 Dihedral : 23.239 179.272 79481 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 6.80 % Allowed : 21.70 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 6269 helix: 2.03 (0.11), residues: 2272 sheet: -0.93 (0.14), residues: 1182 loop : -0.80 (0.11), residues: 2815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 248 HIS 0.011 0.001 HIS w 74 PHE 0.016 0.001 PHE k 8 TYR 0.018 0.002 TYR S 38 ARG 0.010 0.000 ARG M 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 1030 time to evaluate : 6.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 31 LYS cc_start: 0.9286 (tttm) cc_final: 0.8971 (tmtm) REVERT: 6 33 LYS cc_start: 0.9176 (mptp) cc_final: 0.8866 (mmtm) REVERT: 7 133 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: 7 157 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6721 (tp30) REVERT: 7 166 ILE cc_start: 0.8117 (mt) cc_final: 0.7895 (mm) REVERT: 7 169 SER cc_start: 0.7591 (m) cc_final: 0.7358 (t) REVERT: 7 172 GLU cc_start: 0.7531 (tt0) cc_final: 0.6993 (tp30) REVERT: 7 182 LYS cc_start: 0.7346 (tttt) cc_final: 0.7055 (mtpt) REVERT: 7 200 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7179 (ttm-80) REVERT: 7 234 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.6122 (tp) REVERT: 7 255 ASN cc_start: 0.8094 (m-40) cc_final: 0.7783 (m-40) REVERT: 7 256 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7951 (ptm160) REVERT: 7 292 LYS cc_start: 0.7741 (ttmp) cc_final: 0.7149 (tttm) REVERT: 7 297 GLU cc_start: 0.7216 (tp30) cc_final: 0.6778 (tm-30) REVERT: 7 303 LYS cc_start: 0.6969 (mttm) cc_final: 0.6608 (mptt) REVERT: 7 310 MET cc_start: 0.7358 (mmp) cc_final: 0.6514 (tpt) REVERT: 7 329 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: 7 352 SER cc_start: 0.8618 (t) cc_final: 0.8359 (t) REVERT: B 97 LYS cc_start: 0.8381 (mptt) cc_final: 0.7781 (ttpt) REVERT: B 111 LYS cc_start: 0.8369 (pttt) cc_final: 0.7806 (ptpp) REVERT: B 115 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7764 (tp40) REVERT: B 161 TYR cc_start: 0.9038 (p90) cc_final: 0.8774 (p90) REVERT: B 188 CYS cc_start: 0.8902 (m) cc_final: 0.8568 (m) REVERT: B 251 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8690 (mm-40) REVERT: B 270 ARG cc_start: 0.8030 (mmm160) cc_final: 0.6849 (ttt-90) REVERT: C 7 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8322 (ttpp) REVERT: C 13 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.9038 (ptm160) REVERT: C 28 GLU cc_start: 0.8345 (tt0) cc_final: 0.8020 (tt0) REVERT: C 30 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7848 (tp30) REVERT: C 105 LYS cc_start: 0.8474 (mttt) cc_final: 0.7969 (mmtt) REVERT: C 165 MET cc_start: 0.8775 (ttt) cc_final: 0.8430 (ttt) REVERT: D 16 GLU cc_start: 0.7954 (tt0) cc_final: 0.7737 (tp30) REVERT: D 40 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8302 (ttp-170) REVERT: D 69 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7068 (ptp-170) REVERT: D 88 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7737 (mmp80) REVERT: D 122 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: D 132 LYS cc_start: 0.7575 (tttm) cc_final: 0.7236 (ttpt) REVERT: D 136 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.6924 (tm130) REVERT: D 139 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7674 (tttp) REVERT: D 155 GLU cc_start: 0.7636 (tp30) cc_final: 0.7325 (mp0) REVERT: D 171 ASP cc_start: 0.8171 (t70) cc_final: 0.7771 (m-30) REVERT: E 115 ARG cc_start: 0.7412 (mmm160) cc_final: 0.7059 (mmm160) REVERT: E 120 LYS cc_start: 0.8765 (mttt) cc_final: 0.8313 (ptmm) REVERT: E 133 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7914 (mtt-85) REVERT: E 165 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7565 (mt-10) REVERT: F 27 LYS cc_start: 0.7038 (mttt) cc_final: 0.6432 (mppt) REVERT: F 95 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8128 (ptt90) REVERT: F 99 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7744 (mtmm) REVERT: F 176 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5338 (ptpt) REVERT: G 11 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7135 (m110) REVERT: G 35 LYS cc_start: 0.7722 (mttt) cc_final: 0.7471 (mttp) REVERT: G 42 LYS cc_start: 0.6628 (tptt) cc_final: 0.6409 (tptp) REVERT: G 66 ASN cc_start: 0.4249 (OUTLIER) cc_final: 0.3787 (p0) REVERT: G 114 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: G 117 LEU cc_start: 0.5459 (mt) cc_final: 0.5014 (OUTLIER) REVERT: G 127 GLU cc_start: 0.5509 (pt0) cc_final: 0.5263 (tp30) REVERT: H 38 MET cc_start: 0.2422 (mtm) cc_final: 0.1867 (mmm) REVERT: I 11 GLN cc_start: 0.3271 (OUTLIER) cc_final: 0.1632 (tm-30) REVERT: J 98 GLU cc_start: 0.8745 (mp0) cc_final: 0.8395 (mp0) REVERT: J 129 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: K 66 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8799 (mtpt) REVERT: K 93 GLN cc_start: 0.8341 (pt0) cc_final: 0.7706 (mm110) REVERT: K 111 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8126 (ttpt) REVERT: K 113 MET cc_start: 0.7939 (tpt) cc_final: 0.7688 (mmm) REVERT: K 114 LYS cc_start: 0.8363 (tttt) cc_final: 0.7865 (mmpt) REVERT: M 60 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: M 75 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8156 (mt-10) REVERT: M 91 TYR cc_start: 0.9334 (p90) cc_final: 0.9128 (p90) REVERT: M 104 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: M 127 LYS cc_start: 0.8348 (ttmp) cc_final: 0.8006 (tttm) REVERT: N 17 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8597 (ttm-80) REVERT: N 32 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8286 (mm-30) REVERT: N 69 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8617 (mmt90) REVERT: O 13 ARG cc_start: 0.8552 (tmm160) cc_final: 0.7986 (ttt90) REVERT: O 16 ARG cc_start: 0.8339 (mmm160) cc_final: 0.7573 (mmt90) REVERT: O 80 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7595 (mt-10) REVERT: P 7 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: P 83 SER cc_start: 0.8472 (t) cc_final: 0.7897 (m) REVERT: Q 13 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7878 (mtp180) REVERT: R 13 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8325 (ttp80) REVERT: R 31 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7745 (mm-30) REVERT: R 70 GLU cc_start: 0.8476 (tt0) cc_final: 0.8247 (tp30) REVERT: R 86 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8621 (mt0) REVERT: S 38 TYR cc_start: 0.8936 (m-80) cc_final: 0.8431 (m-80) REVERT: S 73 LYS cc_start: 0.8493 (mttt) cc_final: 0.8053 (mtpp) REVERT: T 33 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7704 (tttp) REVERT: T 49 LYS cc_start: 0.8254 (tttt) cc_final: 0.8047 (tttp) REVERT: U 6 ARG cc_start: 0.8241 (mtt180) cc_final: 0.8015 (mtt180) REVERT: U 47 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8030 (ttmm) REVERT: V 7 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: V 12 GLN cc_start: 0.8542 (mt0) cc_final: 0.8279 (mt0) REVERT: W 68 LYS cc_start: 0.8674 (tptp) cc_final: 0.8205 (tppt) REVERT: W 70 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: X 65 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: Y 6 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7659 (mt) REVERT: Y 23 ARG cc_start: 0.8353 (mtm180) cc_final: 0.7923 (mtt90) REVERT: Z 47 MET cc_start: 0.8930 (mtm) cc_final: 0.8383 (mtm) REVERT: Z 56 LYS cc_start: 0.8229 (pttt) cc_final: 0.7834 (pttp) REVERT: Z 58 GLU cc_start: 0.7330 (tt0) cc_final: 0.6935 (tt0) REVERT: b 40 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.6838 (mmp-170) REVERT: d 1 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7849 (mtp) REVERT: d 14 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8378 (mtt-85) REVERT: e 30 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.8015 (mpt90) REVERT: f 8 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8590 (mtpt) REVERT: g 37 LYS cc_start: 0.7139 (tptt) cc_final: 0.6737 (mppt) REVERT: g 63 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.7173 (ttp80) REVERT: g 105 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7374 (tttm) REVERT: g 137 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.5877 (tpp80) REVERT: g 138 THR cc_start: 0.6811 (m) cc_final: 0.6469 (p) REVERT: g 146 ASN cc_start: 0.7156 (m-40) cc_final: 0.6171 (OUTLIER) REVERT: h 85 GLU cc_start: 0.7472 (tp30) cc_final: 0.7048 (mm-30) REVERT: h 89 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7336 (ptpp) REVERT: h 110 GLU cc_start: 0.7694 (mp0) cc_final: 0.7399 (mp0) REVERT: h 118 ASP cc_start: 0.7403 (m-30) cc_final: 0.6643 (m-30) REVERT: h 121 THR cc_start: 0.8878 (m) cc_final: 0.8332 (m) REVERT: h 147 LYS cc_start: 0.8796 (mmpt) cc_final: 0.8527 (mmpt) REVERT: h 187 SER cc_start: 0.9032 (t) cc_final: 0.8626 (t) REVERT: h 193 TYR cc_start: 0.8402 (m-80) cc_final: 0.8177 (m-10) REVERT: h 200 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8607 (t) REVERT: i 45 LYS cc_start: 0.7909 (mttm) cc_final: 0.7607 (mtpm) REVERT: i 60 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8520 (ttpt) REVERT: i 70 ARG cc_start: 0.8717 (tpp80) cc_final: 0.7600 (ttp-110) REVERT: i 142 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8479 (t) REVERT: i 172 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7270 (tm-30) REVERT: i 187 GLU cc_start: 0.8055 (tt0) cc_final: 0.7621 (mm-30) REVERT: j 26 LYS cc_start: 0.9091 (ttpm) cc_final: 0.8784 (ttmm) REVERT: j 45 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7777 (mtm180) REVERT: j 115 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8270 (mt) REVERT: k 7 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8726 (t) REVERT: l 21 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: l 42 ILE cc_start: 0.8856 (mt) cc_final: 0.8479 (mp) REVERT: l 48 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: l 52 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: l 58 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: l 78 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5903 (tmt-80) REVERT: l 79 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.5311 (tmt170) REVERT: l 129 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7472 (mm-30) REVERT: l 130 ASN cc_start: 0.8082 (t0) cc_final: 0.7815 (t0) REVERT: m 4 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8649 (mp10) REVERT: m 31 LYS cc_start: 0.8521 (ttpm) cc_final: 0.8097 (ptmm) REVERT: m 50 LYS cc_start: 0.8141 (tttp) cc_final: 0.7557 (tptm) REVERT: m 51 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8094 (t) REVERT: m 58 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8100 (mt-10) REVERT: n 22 LYS cc_start: 0.7480 (tttt) cc_final: 0.7065 (mttm) REVERT: n 33 ARG cc_start: 0.7650 (mtt90) cc_final: 0.7218 (mtm180) REVERT: n 42 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7409 (mm-30) REVERT: n 57 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6261 (mtm) REVERT: n 64 TYR cc_start: 0.8765 (t80) cc_final: 0.8483 (t80) REVERT: n 124 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8413 (mtm-85) REVERT: o 7 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6763 (mmm160) REVERT: o 60 ASP cc_start: 0.8720 (m-30) cc_final: 0.8435 (m-30) REVERT: o 97 ASP cc_start: 0.7592 (t70) cc_final: 0.7389 (t0) REVERT: p 18 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: p 69 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7236 (mmm160) REVERT: p 76 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: p 119 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7389 (t0) REVERT: q 9 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7834 (ttm170) REVERT: q 25 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8229 (mm-30) REVERT: q 76 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7954 (tt0) REVERT: q 108 LYS cc_start: 0.8584 (mttt) cc_final: 0.8127 (mmtm) REVERT: r 76 SER cc_start: 0.8088 (m) cc_final: 0.7717 (p) REVERT: r 93 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7803 (mmp80) REVERT: t 40 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: u 42 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8485 (mp) REVERT: u 47 GLU cc_start: 0.7836 (pt0) cc_final: 0.7521 (pt0) REVERT: u 63 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: w 35 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: w 48 ARG cc_start: 0.7724 (mtm110) cc_final: 0.6656 (mmt90) REVERT: x 17 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7501 (mmpt) REVERT: x 21 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6884 (mtmt) REVERT: x 32 ARG cc_start: 0.8185 (ptt180) cc_final: 0.7749 (ptp-170) REVERT: x 63 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7613 (p) REVERT: y 48 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7714 (tp40) REVERT: y 49 LYS cc_start: 0.8191 (tppt) cc_final: 0.7897 (ttmt) REVERT: y 85 LYS cc_start: 0.7311 (tttt) cc_final: 0.6836 (mmmm) REVERT: z 31 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7407 (tp30) REVERT: z 33 ARG cc_start: 0.8011 (tmt170) cc_final: 0.7530 (ttm170) REVERT: z 55 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.6906 (mmt180) outliers start: 355 outliers final: 191 residues processed: 1241 average time/residue: 2.2381 time to fit residues: 3968.6741 Evaluate side-chains 1275 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1014 time to evaluate : 6.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 42 LYS Chi-restraints excluded: chain 7 residue 42 GLU Chi-restraints excluded: chain 7 residue 110 LEU Chi-restraints excluded: chain 7 residue 133 GLN Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 240 ARG Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 268 THR Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain 7 residue 360 SER Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 45 LYS Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 206 GLU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 60 LYS Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 52 GLN Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 4 GLN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 48 LYS Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain u residue 63 GLN Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 48 GLN Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 31 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 349 optimal weight: 10.0000 chunk 935 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 610 optimal weight: 20.0000 chunk 256 optimal weight: 7.9990 chunk 1040 optimal weight: 10.0000 chunk 863 optimal weight: 20.0000 chunk 481 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 546 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN E 23 ASN F 104 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN N 18 GLN O 100 HIS Q 20 GLN Q 72 ASN Y 27 ASN h 102 ASN l 148 ASN p 28 ASN s 49 GLN u 18 GLN v 9 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 43 ASN y 84 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 162068 Z= 0.497 Angle : 0.756 16.187 241755 Z= 0.395 Chirality : 0.045 0.362 30685 Planarity : 0.007 0.145 13434 Dihedral : 23.276 179.156 79470 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 7.65 % Allowed : 21.58 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 6269 helix: 1.57 (0.11), residues: 2266 sheet: -0.95 (0.14), residues: 1201 loop : -0.86 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 248 HIS 0.008 0.002 HIS B 230 PHE 0.021 0.002 PHE j 33 TYR 0.021 0.003 TYR i 103 ARG 0.015 0.001 ARG o 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 1006 time to evaluate : 6.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 33 LYS cc_start: 0.9275 (mptp) cc_final: 0.8892 (mmtp) REVERT: 7 133 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: 7 157 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6757 (tp30) REVERT: 7 169 SER cc_start: 0.7558 (m) cc_final: 0.7352 (t) REVERT: 7 172 GLU cc_start: 0.7613 (tt0) cc_final: 0.7007 (tp30) REVERT: 7 182 LYS cc_start: 0.7366 (tttt) cc_final: 0.7065 (mtpt) REVERT: 7 200 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7234 (ttm-80) REVERT: 7 234 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6229 (tp) REVERT: 7 255 ASN cc_start: 0.8056 (m-40) cc_final: 0.7677 (m-40) REVERT: 7 292 LYS cc_start: 0.7700 (ttmp) cc_final: 0.6990 (tmtm) REVERT: 7 297 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: 7 303 LYS cc_start: 0.6963 (mttm) cc_final: 0.6593 (mptt) REVERT: 7 310 MET cc_start: 0.7391 (mmp) cc_final: 0.7124 (mmm) REVERT: 7 352 SER cc_start: 0.8496 (t) cc_final: 0.8218 (t) REVERT: B 23 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: B 97 LYS cc_start: 0.8446 (mptt) cc_final: 0.7846 (ttpt) REVERT: B 111 LYS cc_start: 0.8401 (pttt) cc_final: 0.8044 (ptpp) REVERT: B 114 ASP cc_start: 0.8099 (m-30) cc_final: 0.7887 (m-30) REVERT: B 115 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: B 161 TYR cc_start: 0.9128 (p90) cc_final: 0.8902 (p90) REVERT: B 188 CYS cc_start: 0.8831 (m) cc_final: 0.8393 (m) REVERT: B 242 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8582 (mptt) REVERT: B 251 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8744 (mm-40) REVERT: B 270 ARG cc_start: 0.8141 (mmm160) cc_final: 0.6926 (ttt-90) REVERT: C 7 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8314 (ttpp) REVERT: C 13 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.9084 (ptm160) REVERT: C 28 GLU cc_start: 0.8373 (tt0) cc_final: 0.8058 (tt0) REVERT: C 30 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7883 (tp30) REVERT: C 105 LYS cc_start: 0.8465 (mttt) cc_final: 0.7979 (mmtt) REVERT: C 131 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: C 165 MET cc_start: 0.8821 (ttt) cc_final: 0.8491 (ttt) REVERT: C 176 ASP cc_start: 0.8618 (t70) cc_final: 0.8288 (m-30) REVERT: D 16 GLU cc_start: 0.7928 (tt0) cc_final: 0.7670 (tp30) REVERT: D 40 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8225 (ttp-170) REVERT: D 69 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7307 (ptp-170) REVERT: D 111 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: D 122 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: D 132 LYS cc_start: 0.7657 (tttm) cc_final: 0.7349 (ttpt) REVERT: D 136 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7017 (tm130) REVERT: D 139 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7640 (tttp) REVERT: D 141 MET cc_start: 0.6792 (mpt) cc_final: 0.6508 (mmt) REVERT: D 155 GLU cc_start: 0.7834 (tp30) cc_final: 0.7429 (mp0) REVERT: D 171 ASP cc_start: 0.8196 (t70) cc_final: 0.7851 (t70) REVERT: D 197 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7333 (tp30) REVERT: E 115 ARG cc_start: 0.7470 (mmm160) cc_final: 0.7079 (mmm160) REVERT: E 120 LYS cc_start: 0.8796 (mttt) cc_final: 0.8328 (ptmt) REVERT: E 133 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7944 (mtt-85) REVERT: E 165 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7542 (mt-10) REVERT: F 27 LYS cc_start: 0.7052 (mttt) cc_final: 0.6447 (mppt) REVERT: F 95 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7931 (ptm-80) REVERT: F 99 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7781 (mtmm) REVERT: F 176 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5394 (ptpt) REVERT: G 11 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7152 (m110) REVERT: G 35 LYS cc_start: 0.7779 (mttt) cc_final: 0.7505 (mttp) REVERT: G 42 LYS cc_start: 0.6604 (tptt) cc_final: 0.6362 (tptp) REVERT: G 66 ASN cc_start: 0.4381 (OUTLIER) cc_final: 0.3926 (p0) REVERT: G 114 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6610 (mm-30) REVERT: G 117 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.5048 (mt) REVERT: G 127 GLU cc_start: 0.5458 (pt0) cc_final: 0.5071 (mp0) REVERT: H 38 MET cc_start: 0.2471 (mtm) cc_final: 0.1903 (mmm) REVERT: I 11 GLN cc_start: 0.2708 (OUTLIER) cc_final: 0.1378 (tm-30) REVERT: J 98 GLU cc_start: 0.8802 (mp0) cc_final: 0.8493 (mp0) REVERT: J 129 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: J 138 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: K 93 GLN cc_start: 0.8448 (pt0) cc_final: 0.7710 (mm110) REVERT: K 111 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (ttpt) REVERT: K 113 MET cc_start: 0.8106 (tpt) cc_final: 0.7838 (mmm) REVERT: K 114 LYS cc_start: 0.8521 (tttt) cc_final: 0.8129 (tptm) REVERT: M 18 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8455 (ptm-80) REVERT: M 60 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: M 91 TYR cc_start: 0.9324 (p90) cc_final: 0.9088 (p90) REVERT: M 103 TYR cc_start: 0.9114 (m-80) cc_final: 0.8653 (m-80) REVERT: M 104 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8576 (mt-10) REVERT: M 127 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7986 (tttm) REVERT: N 32 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8339 (mm-30) REVERT: O 13 ARG cc_start: 0.8591 (tmm160) cc_final: 0.8013 (ttt90) REVERT: O 16 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7454 (mmt90) REVERT: O 80 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7584 (mt-10) REVERT: P 83 SER cc_start: 0.8611 (t) cc_final: 0.8298 (p) REVERT: P 103 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8214 (mmm-85) REVERT: Q 13 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8072 (mtp180) REVERT: R 19 THR cc_start: 0.8909 (m) cc_final: 0.8475 (t) REVERT: R 31 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7880 (mm-30) REVERT: R 70 GLU cc_start: 0.8489 (tt0) cc_final: 0.8222 (tp30) REVERT: R 86 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8641 (mt0) REVERT: S 38 TYR cc_start: 0.9064 (m-80) cc_final: 0.8539 (m-80) REVERT: S 73 LYS cc_start: 0.8526 (mttt) cc_final: 0.8093 (mtpp) REVERT: T 33 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7779 (tttm) REVERT: T 49 LYS cc_start: 0.8324 (tttt) cc_final: 0.7970 (tttp) REVERT: U 6 ARG cc_start: 0.8296 (mtt180) cc_final: 0.8036 (mtt180) REVERT: U 47 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8092 (ttmm) REVERT: V 7 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: V 12 GLN cc_start: 0.8519 (mt0) cc_final: 0.8312 (mt0) REVERT: W 68 LYS cc_start: 0.8749 (tptp) cc_final: 0.8237 (tppt) REVERT: Y 2 LYS cc_start: 0.6894 (mtpt) cc_final: 0.6015 (tttm) REVERT: Y 5 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7150 (pp20) REVERT: Y 6 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7473 (mt) REVERT: Y 23 ARG cc_start: 0.8353 (mtm180) cc_final: 0.7934 (mtt90) REVERT: Z 56 LYS cc_start: 0.8287 (pttt) cc_final: 0.7899 (pttp) REVERT: Z 58 GLU cc_start: 0.7362 (tt0) cc_final: 0.6882 (tt0) REVERT: b 40 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7082 (mmt180) REVERT: d 14 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8483 (mtt-85) REVERT: e 15 LYS cc_start: 0.8630 (mptt) cc_final: 0.8415 (mptt) REVERT: f 8 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8584 (mtpt) REVERT: g 36 ASN cc_start: 0.7731 (t0) cc_final: 0.7407 (t0) REVERT: g 37 LYS cc_start: 0.7041 (tptt) cc_final: 0.6651 (mmtt) REVERT: g 63 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7149 (ttp80) REVERT: g 105 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7498 (tttm) REVERT: g 137 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5969 (tpp80) REVERT: g 138 THR cc_start: 0.6839 (m) cc_final: 0.6491 (p) REVERT: g 146 ASN cc_start: 0.7242 (m-40) cc_final: 0.6233 (OUTLIER) REVERT: h 27 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7437 (mptt) REVERT: h 85 GLU cc_start: 0.7464 (tp30) cc_final: 0.6950 (mm-30) REVERT: h 89 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7339 (ptpp) REVERT: h 110 GLU cc_start: 0.7748 (mp0) cc_final: 0.7526 (mp0) REVERT: h 121 THR cc_start: 0.8867 (m) cc_final: 0.8284 (m) REVERT: h 147 LYS cc_start: 0.8811 (mmpt) cc_final: 0.8474 (mmmt) REVERT: h 187 SER cc_start: 0.9011 (t) cc_final: 0.8658 (t) REVERT: h 193 TYR cc_start: 0.8327 (m-80) cc_final: 0.8078 (m-10) REVERT: i 45 LYS cc_start: 0.7856 (mttm) cc_final: 0.7567 (mtpm) REVERT: i 70 ARG cc_start: 0.8745 (tpp80) cc_final: 0.7667 (ttp-110) REVERT: i 172 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7288 (tm-30) REVERT: i 187 GLU cc_start: 0.8029 (tt0) cc_final: 0.7597 (mm-30) REVERT: j 13 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: j 26 LYS cc_start: 0.9122 (ttpm) cc_final: 0.8771 (ttmm) REVERT: j 115 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8310 (mt) REVERT: k 7 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8633 (t) REVERT: l 21 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: l 52 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6721 (mp10) REVERT: l 58 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: l 78 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.5816 (tmt-80) REVERT: l 79 ARG cc_start: 0.5987 (OUTLIER) cc_final: 0.5311 (tmt170) REVERT: l 129 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7431 (mm-30) REVERT: l 130 ASN cc_start: 0.8104 (t0) cc_final: 0.7847 (t0) REVERT: l 144 MET cc_start: 0.7211 (ttt) cc_final: 0.6858 (ttt) REVERT: l 148 ASN cc_start: 0.8430 (m-40) cc_final: 0.8012 (m-40) REVERT: m 4 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8767 (mp10) REVERT: m 43 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: m 50 LYS cc_start: 0.8196 (tttp) cc_final: 0.7602 (tptm) REVERT: m 58 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7995 (tt0) REVERT: n 33 ARG cc_start: 0.7600 (mtt90) cc_final: 0.7162 (mtm180) REVERT: n 42 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7483 (mm-30) REVERT: n 57 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6305 (mtm) REVERT: n 64 TYR cc_start: 0.8815 (t80) cc_final: 0.8589 (t80) REVERT: n 98 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7157 (mm) REVERT: o 7 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6926 (mmm160) REVERT: o 60 ASP cc_start: 0.8709 (m-30) cc_final: 0.8420 (m-30) REVERT: o 97 ASP cc_start: 0.7700 (t70) cc_final: 0.7495 (t0) REVERT: p 18 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: p 69 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7228 (mmm160) REVERT: p 76 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: q 9 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7950 (ttm110) REVERT: q 25 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8211 (mm-30) REVERT: q 44 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8450 (tppp) REVERT: q 76 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7925 (tt0) REVERT: q 108 LYS cc_start: 0.8630 (mttt) cc_final: 0.8168 (mmtm) REVERT: r 29 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7479 (mtt180) REVERT: r 48 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6882 (mp) REVERT: r 76 SER cc_start: 0.8088 (m) cc_final: 0.7751 (p) REVERT: r 81 MET cc_start: 0.8339 (mtt) cc_final: 0.7921 (mtt) REVERT: s 40 ASP cc_start: 0.7782 (m-30) cc_final: 0.7552 (m-30) REVERT: s 65 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7323 (mtt90) REVERT: t 83 GLU cc_start: 0.8378 (tt0) cc_final: 0.8058 (tt0) REVERT: u 42 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8600 (mp) REVERT: u 63 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: w 35 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: w 48 ARG cc_start: 0.7805 (mtm110) cc_final: 0.6688 (mmt90) REVERT: x 17 LYS cc_start: 0.7934 (mmmm) cc_final: 0.7477 (mmpt) REVERT: x 21 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6722 (mtmt) REVERT: x 32 ARG cc_start: 0.8173 (ptt180) cc_final: 0.7748 (ptp-170) REVERT: x 63 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7712 (p) REVERT: y 48 GLN cc_start: 0.8024 (mm110) cc_final: 0.7621 (mm-40) REVERT: y 49 LYS cc_start: 0.8197 (tppt) cc_final: 0.7817 (ttmm) REVERT: y 85 LYS cc_start: 0.7470 (tttt) cc_final: 0.6983 (mmmm) REVERT: z 31 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: z 33 ARG cc_start: 0.8021 (tmt170) cc_final: 0.7496 (ttm170) REVERT: z 55 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.6747 (mmt180) outliers start: 399 outliers final: 228 residues processed: 1236 average time/residue: 2.2671 time to fit residues: 4003.1959 Evaluate side-chains 1288 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 992 time to evaluate : 6.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 42 LYS Chi-restraints excluded: chain 7 residue 110 LEU Chi-restraints excluded: chain 7 residue 133 GLN Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 240 ARG Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 268 THR Chi-restraints excluded: chain 7 residue 297 GLU Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain 7 residue 360 SER Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 45 LYS Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 72 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 52 GLN Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 4 GLN Chi-restraints excluded: chain m residue 43 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 57 MET Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 29 ARG Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 65 ARG Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 12 LYS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain u residue 63 GLN Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 31 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 1002 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 592 optimal weight: 5.9990 chunk 759 optimal weight: 4.9990 chunk 588 optimal weight: 5.9990 chunk 875 optimal weight: 3.9990 chunk 580 optimal weight: 2.9990 chunk 1036 optimal weight: 2.9990 chunk 648 optimal weight: 1.9990 chunk 631 optimal weight: 2.9990 chunk 478 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 304 ASN 7 313 ASN E 23 ASN E 63 GLN F 104 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 93 ASN N 18 GLN O 100 HIS ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN Y 27 ASN h 102 ASN ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 28 ASN s 49 GLN w 74 HIS w 75 GLN x 14 HIS x 43 ASN y 84 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 162068 Z= 0.266 Angle : 0.652 15.800 241755 Z= 0.351 Chirality : 0.038 0.385 30685 Planarity : 0.006 0.133 13434 Dihedral : 23.324 178.881 79457 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 6.38 % Allowed : 23.29 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.10), residues: 6269 helix: 1.73 (0.11), residues: 2269 sheet: -0.92 (0.14), residues: 1209 loop : -0.79 (0.11), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 248 HIS 0.007 0.001 HIS w 74 PHE 0.022 0.002 PHE a 64 TYR 0.026 0.002 TYR h 42 ARG 0.013 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1017 time to evaluate : 6.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 33 LYS cc_start: 0.9253 (mptp) cc_final: 0.8923 (mmtp) REVERT: 7 133 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: 7 157 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6724 (tp30) REVERT: 7 172 GLU cc_start: 0.7541 (tt0) cc_final: 0.6936 (tp30) REVERT: 7 182 LYS cc_start: 0.7325 (tttt) cc_final: 0.7006 (mtpt) REVERT: 7 200 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7143 (ttm-80) REVERT: 7 234 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6093 (tp) REVERT: 7 255 ASN cc_start: 0.8139 (m-40) cc_final: 0.7789 (m-40) REVERT: 7 256 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7972 (ptm160) REVERT: 7 292 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7033 (tmtm) REVERT: 7 297 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: 7 299 GLU cc_start: 0.7109 (tt0) cc_final: 0.6325 (mp0) REVERT: 7 303 LYS cc_start: 0.6976 (mttm) cc_final: 0.6609 (mptt) REVERT: 7 310 MET cc_start: 0.7368 (mmp) cc_final: 0.6689 (mmm) REVERT: 7 352 SER cc_start: 0.8579 (t) cc_final: 0.8296 (t) REVERT: B 23 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 97 LYS cc_start: 0.8442 (mptt) cc_final: 0.7819 (ttpt) REVERT: B 111 LYS cc_start: 0.8334 (pttt) cc_final: 0.7983 (ptpp) REVERT: B 115 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7934 (tp40) REVERT: B 133 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7475 (ptp90) REVERT: B 161 TYR cc_start: 0.9075 (p90) cc_final: 0.8846 (p90) REVERT: B 188 CYS cc_start: 0.8808 (m) cc_final: 0.8437 (m) REVERT: B 251 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8677 (mm-40) REVERT: B 270 ARG cc_start: 0.8102 (mmm160) cc_final: 0.6875 (ttt-90) REVERT: C 7 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8333 (ttpp) REVERT: C 13 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8996 (ptm160) REVERT: C 28 GLU cc_start: 0.8331 (tt0) cc_final: 0.7974 (tt0) REVERT: C 30 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7902 (tp30) REVERT: C 105 LYS cc_start: 0.8457 (mttt) cc_final: 0.7974 (mmtt) REVERT: C 165 MET cc_start: 0.8788 (ttt) cc_final: 0.8446 (ttt) REVERT: C 176 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: D 16 GLU cc_start: 0.7900 (tt0) cc_final: 0.7664 (tp30) REVERT: D 40 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8291 (ttp-170) REVERT: D 69 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7220 (ptp-170) REVERT: D 88 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7811 (mmp80) REVERT: D 122 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: D 132 LYS cc_start: 0.7593 (tttm) cc_final: 0.7233 (ttpt) REVERT: D 136 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: D 139 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7645 (tttp) REVERT: D 155 GLU cc_start: 0.7763 (tp30) cc_final: 0.7401 (mp0) REVERT: D 171 ASP cc_start: 0.8202 (t70) cc_final: 0.7768 (m-30) REVERT: D 197 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7359 (tp30) REVERT: E 71 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7957 (ttp80) REVERT: E 115 ARG cc_start: 0.7454 (mmm160) cc_final: 0.7079 (mmm160) REVERT: E 120 LYS cc_start: 0.8763 (mttt) cc_final: 0.8314 (ptmt) REVERT: E 133 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7904 (mtt-85) REVERT: E 165 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7541 (mt-10) REVERT: F 27 LYS cc_start: 0.7039 (mttt) cc_final: 0.6432 (mppt) REVERT: F 95 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7898 (ptm-80) REVERT: F 99 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7763 (mtmm) REVERT: F 176 LYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5364 (ptpt) REVERT: G 11 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7149 (m110) REVERT: G 35 LYS cc_start: 0.7716 (mttt) cc_final: 0.7488 (mttp) REVERT: G 42 LYS cc_start: 0.6594 (tptt) cc_final: 0.6316 (tptp) REVERT: G 66 ASN cc_start: 0.4368 (OUTLIER) cc_final: 0.3918 (p0) REVERT: G 114 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: G 117 LEU cc_start: 0.5442 (mt) cc_final: 0.5023 (mt) REVERT: G 127 GLU cc_start: 0.5411 (pt0) cc_final: 0.5047 (mp0) REVERT: H 38 MET cc_start: 0.2447 (mtm) cc_final: 0.1939 (mmm) REVERT: J 35 ARG cc_start: 0.8744 (mtt90) cc_final: 0.8424 (mtp85) REVERT: J 98 GLU cc_start: 0.8745 (mp0) cc_final: 0.8382 (mp0) REVERT: J 129 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: K 93 GLN cc_start: 0.8406 (pt0) cc_final: 0.7690 (mm110) REVERT: K 111 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8246 (ttpt) REVERT: K 113 MET cc_start: 0.8098 (tpt) cc_final: 0.7857 (mmm) REVERT: K 114 LYS cc_start: 0.8496 (tttt) cc_final: 0.8120 (tptm) REVERT: M 6 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7143 (mtm-85) REVERT: M 60 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: M 75 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8166 (mt-10) REVERT: M 91 TYR cc_start: 0.9323 (p90) cc_final: 0.9105 (p90) REVERT: M 103 TYR cc_start: 0.9090 (m-80) cc_final: 0.8617 (m-80) REVERT: M 104 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: M 127 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7945 (tttm) REVERT: N 17 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8617 (ttm-80) REVERT: N 32 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8303 (mm-30) REVERT: O 13 ARG cc_start: 0.8567 (tmm160) cc_final: 0.7981 (ttt90) REVERT: O 16 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7535 (mmt90) REVERT: O 80 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7574 (mt-10) REVERT: P 7 GLN cc_start: 0.8064 (tp40) cc_final: 0.7566 (tm-30) REVERT: P 83 SER cc_start: 0.8538 (t) cc_final: 0.7873 (m) REVERT: Q 13 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7994 (mtp180) REVERT: R 19 THR cc_start: 0.8904 (m) cc_final: 0.8473 (t) REVERT: R 70 GLU cc_start: 0.8494 (tt0) cc_final: 0.8228 (tp30) REVERT: R 86 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: S 38 TYR cc_start: 0.8958 (m-80) cc_final: 0.8458 (m-80) REVERT: S 73 LYS cc_start: 0.8435 (mttt) cc_final: 0.8010 (mtpp) REVERT: T 33 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7670 (tttp) REVERT: U 6 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7945 (mtt180) REVERT: U 47 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8030 (ttmm) REVERT: V 7 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: V 12 GLN cc_start: 0.8496 (mt0) cc_final: 0.8176 (mt0) REVERT: W 68 LYS cc_start: 0.8698 (tptp) cc_final: 0.8215 (tppt) REVERT: Y 2 LYS cc_start: 0.6850 (mtpt) cc_final: 0.5985 (tttm) REVERT: Y 5 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7151 (pp20) REVERT: Y 6 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7387 (mt) REVERT: Y 23 ARG cc_start: 0.8337 (mtm180) cc_final: 0.7933 (mtt90) REVERT: Z 56 LYS cc_start: 0.8261 (pttt) cc_final: 0.7876 (pttp) REVERT: Z 58 GLU cc_start: 0.7366 (tt0) cc_final: 0.6864 (tt0) REVERT: d 14 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8350 (mtt-85) REVERT: f 8 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8551 (mtpt) REVERT: g 37 LYS cc_start: 0.7113 (tptt) cc_final: 0.6684 (mmtt) REVERT: g 63 ARG cc_start: 0.7407 (ttp-110) cc_final: 0.7120 (ttp80) REVERT: g 105 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7424 (tttm) REVERT: g 137 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.5963 (tpp80) REVERT: g 138 THR cc_start: 0.6835 (m) cc_final: 0.6486 (p) REVERT: g 146 ASN cc_start: 0.7188 (m-40) cc_final: 0.6194 (OUTLIER) REVERT: h 85 GLU cc_start: 0.7424 (tp30) cc_final: 0.6967 (mm-30) REVERT: h 89 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7336 (ptpp) REVERT: h 110 GLU cc_start: 0.7728 (mp0) cc_final: 0.7426 (mp0) REVERT: h 121 THR cc_start: 0.8888 (m) cc_final: 0.8337 (m) REVERT: h 147 LYS cc_start: 0.8813 (mmpt) cc_final: 0.8480 (mmmt) REVERT: h 164 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8579 (ptt-90) REVERT: h 187 SER cc_start: 0.8983 (t) cc_final: 0.8607 (t) REVERT: h 193 TYR cc_start: 0.8355 (m-80) cc_final: 0.8104 (m-10) REVERT: h 200 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8573 (t) REVERT: i 45 LYS cc_start: 0.7841 (mttm) cc_final: 0.7565 (mtpm) REVERT: i 70 ARG cc_start: 0.8762 (tpp80) cc_final: 0.7653 (ttp-110) REVERT: i 172 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7269 (tm-30) REVERT: i 187 GLU cc_start: 0.8029 (tt0) cc_final: 0.7608 (mm-30) REVERT: j 13 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7952 (pt0) REVERT: j 26 LYS cc_start: 0.9115 (ttpm) cc_final: 0.8757 (ttmm) REVERT: j 115 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8251 (mt) REVERT: k 7 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8671 (t) REVERT: l 21 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: l 52 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6889 (mp10) REVERT: l 58 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: l 78 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.5829 (tmt-80) REVERT: l 79 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5284 (tmt170) REVERT: l 129 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7437 (mm-30) REVERT: l 130 ASN cc_start: 0.8044 (t0) cc_final: 0.7830 (t0) REVERT: l 148 ASN cc_start: 0.8384 (m-40) cc_final: 0.8023 (m-40) REVERT: m 4 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: m 31 LYS cc_start: 0.8501 (ttpp) cc_final: 0.8216 (ptmm) REVERT: m 43 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: m 50 LYS cc_start: 0.8154 (tttp) cc_final: 0.7587 (tptm) REVERT: m 58 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8090 (mt-10) REVERT: m 118 GLN cc_start: 0.7771 (tt0) cc_final: 0.7476 (mt0) REVERT: n 33 ARG cc_start: 0.7620 (mtt90) cc_final: 0.7190 (mtm180) REVERT: n 42 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7414 (mm-30) REVERT: n 64 TYR cc_start: 0.8797 (t80) cc_final: 0.8526 (t80) REVERT: n 98 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7156 (mm) REVERT: n 124 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.8410 (mtm-85) REVERT: o 7 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6640 (mtp180) REVERT: o 60 ASP cc_start: 0.8690 (m-30) cc_final: 0.8396 (m-30) REVERT: p 18 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: p 69 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7176 (mmm160) REVERT: p 76 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: q 9 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7836 (ttm110) REVERT: q 15 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.5716 (mtpp) REVERT: q 25 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8193 (mm-30) REVERT: q 44 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8497 (tppp) REVERT: q 76 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7929 (tt0) REVERT: q 108 LYS cc_start: 0.8610 (mttt) cc_final: 0.8151 (mmtm) REVERT: r 29 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7370 (mtt180) REVERT: r 76 SER cc_start: 0.8128 (m) cc_final: 0.7756 (p) REVERT: r 93 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7901 (mmp80) REVERT: s 40 ASP cc_start: 0.7780 (m-30) cc_final: 0.7540 (m-30) REVERT: t 40 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: t 83 GLU cc_start: 0.8393 (tt0) cc_final: 0.8081 (tt0) REVERT: u 42 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8487 (mp) REVERT: u 51 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.7815 (ttp80) REVERT: w 35 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: w 48 ARG cc_start: 0.7754 (mtm110) cc_final: 0.6672 (mmt90) REVERT: x 17 LYS cc_start: 0.7874 (mmmm) cc_final: 0.7522 (mmpt) REVERT: x 21 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6742 (mtmt) REVERT: x 32 ARG cc_start: 0.8139 (ptt180) cc_final: 0.7711 (ptp-170) REVERT: x 63 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7686 (p) REVERT: y 48 GLN cc_start: 0.8050 (mm110) cc_final: 0.7635 (mm-40) REVERT: y 49 LYS cc_start: 0.8177 (tppt) cc_final: 0.7787 (ttmm) REVERT: y 85 LYS cc_start: 0.7343 (tttt) cc_final: 0.6844 (mmmm) REVERT: z 31 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: z 33 ARG cc_start: 0.8034 (tmt170) cc_final: 0.7494 (ttm170) REVERT: z 55 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.6734 (mmt180) outliers start: 333 outliers final: 207 residues processed: 1215 average time/residue: 2.2371 time to fit residues: 3885.5802 Evaluate side-chains 1266 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 994 time to evaluate : 6.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 42 LYS Chi-restraints excluded: chain 7 residue 133 GLN Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 240 ARG Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 268 THR Chi-restraints excluded: chain 7 residue 297 GLU Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 45 LYS Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 153 ASP Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 72 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 182 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 52 GLN Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 4 GLN Chi-restraints excluded: chain m residue 43 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 15 LYS Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 75 GLN Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 29 ARG Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain u residue 63 GLN Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 35 SER Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 31 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 641 optimal weight: 0.9980 chunk 413 optimal weight: 6.9990 chunk 618 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 658 optimal weight: 7.9990 chunk 705 optimal weight: 10.0000 chunk 512 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 814 optimal weight: 9.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 304 ASN 7 313 ASN E 23 ASN E 63 GLN F 104 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 93 ASN N 18 GLN Q 20 GLN Y 27 ASN e 28 ASN h 102 ASN ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 28 ASN p 119 ASN u 29 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 84 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 162068 Z= 0.372 Angle : 0.685 15.870 241755 Z= 0.363 Chirality : 0.040 0.369 30685 Planarity : 0.007 0.139 13434 Dihedral : 23.242 179.958 79456 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 6.48 % Allowed : 23.35 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 6269 helix: 1.63 (0.11), residues: 2269 sheet: -0.88 (0.14), residues: 1212 loop : -0.80 (0.11), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 248 HIS 0.012 0.001 HIS w 74 PHE 0.019 0.002 PHE a 64 TYR 0.024 0.002 TYR h 42 ARG 0.010 0.001 ARG o 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 992 time to evaluate : 6.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 30 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: 6 33 LYS cc_start: 0.9194 (mptp) cc_final: 0.8859 (mmtm) REVERT: 7 133 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: 7 157 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6762 (tp30) REVERT: 7 172 GLU cc_start: 0.7554 (tt0) cc_final: 0.6918 (tp30) REVERT: 7 182 LYS cc_start: 0.7342 (tttt) cc_final: 0.7060 (mtpt) REVERT: 7 200 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7095 (ttm-80) REVERT: 7 234 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.6096 (tp) REVERT: 7 255 ASN cc_start: 0.7964 (m-40) cc_final: 0.7594 (m-40) REVERT: 7 256 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7964 (ptm160) REVERT: 7 292 LYS cc_start: 0.7692 (ttmp) cc_final: 0.7110 (tttm) REVERT: 7 297 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: 7 303 LYS cc_start: 0.6981 (mttm) cc_final: 0.6614 (mptt) REVERT: 7 310 MET cc_start: 0.7387 (mmp) cc_final: 0.6682 (mmm) REVERT: 7 352 SER cc_start: 0.8585 (t) cc_final: 0.8303 (t) REVERT: B 23 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: B 97 LYS cc_start: 0.8450 (mptt) cc_final: 0.7798 (ttpt) REVERT: B 111 LYS cc_start: 0.8287 (pttt) cc_final: 0.7943 (ptpp) REVERT: B 115 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7981 (tp40) REVERT: B 133 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7417 (ptp90) REVERT: B 161 TYR cc_start: 0.9087 (p90) cc_final: 0.8853 (p90) REVERT: B 188 CYS cc_start: 0.8849 (m) cc_final: 0.8480 (m) REVERT: B 251 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8714 (mm-40) REVERT: B 270 ARG cc_start: 0.8153 (mmm160) cc_final: 0.6911 (ttt-90) REVERT: C 7 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8377 (ttpp) REVERT: C 13 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.9016 (ptm160) REVERT: C 28 GLU cc_start: 0.8341 (tt0) cc_final: 0.8028 (tt0) REVERT: C 30 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7917 (tp30) REVERT: C 33 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7825 (ptt90) REVERT: C 165 MET cc_start: 0.8813 (ttt) cc_final: 0.8470 (ttt) REVERT: C 176 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8270 (m-30) REVERT: D 16 GLU cc_start: 0.7918 (tt0) cc_final: 0.7680 (tp30) REVERT: D 40 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8257 (ttp-170) REVERT: D 69 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7256 (ptp-170) REVERT: D 88 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7840 (mmp80) REVERT: D 111 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: D 122 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: D 132 LYS cc_start: 0.7673 (tttm) cc_final: 0.7381 (ttpt) REVERT: D 136 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: D 139 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7651 (tttp) REVERT: D 141 MET cc_start: 0.6747 (mpt) cc_final: 0.6491 (mmt) REVERT: D 155 GLU cc_start: 0.7866 (tp30) cc_final: 0.7412 (mp0) REVERT: D 171 ASP cc_start: 0.8225 (t70) cc_final: 0.7884 (t70) REVERT: D 197 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7461 (tp30) REVERT: E 32 GLU cc_start: 0.8065 (tt0) cc_final: 0.7836 (tt0) REVERT: E 115 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7181 (mmm160) REVERT: E 120 LYS cc_start: 0.8777 (mttt) cc_final: 0.8321 (ptmt) REVERT: E 133 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7919 (mtt-85) REVERT: E 165 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7546 (mt-10) REVERT: F 27 LYS cc_start: 0.7030 (mttt) cc_final: 0.6443 (mppt) REVERT: F 95 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7907 (ptm-80) REVERT: F 99 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7794 (mtmm) REVERT: F 176 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5340 (ptpt) REVERT: G 11 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7249 (m110) REVERT: G 35 LYS cc_start: 0.7738 (mttt) cc_final: 0.7509 (mttp) REVERT: G 42 LYS cc_start: 0.6528 (tptt) cc_final: 0.6259 (tptp) REVERT: G 66 ASN cc_start: 0.4410 (OUTLIER) cc_final: 0.3984 (p0) REVERT: G 114 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: G 117 LEU cc_start: 0.5424 (mt) cc_final: 0.5003 (mt) REVERT: G 127 GLU cc_start: 0.5477 (pt0) cc_final: 0.5040 (mp0) REVERT: H 38 MET cc_start: 0.2364 (mtm) cc_final: 0.1850 (mmm) REVERT: J 35 ARG cc_start: 0.8737 (mtt90) cc_final: 0.8433 (mtp85) REVERT: J 98 GLU cc_start: 0.8723 (mp0) cc_final: 0.8441 (mp0) REVERT: J 108 MET cc_start: 0.9015 (mtt) cc_final: 0.8617 (mtt) REVERT: J 129 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: K 93 GLN cc_start: 0.8423 (pt0) cc_final: 0.7729 (mm110) REVERT: K 113 MET cc_start: 0.8080 (tpt) cc_final: 0.7841 (mmm) REVERT: K 114 LYS cc_start: 0.8511 (tttt) cc_final: 0.8126 (tptm) REVERT: M 60 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7668 (mp10) REVERT: M 75 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8167 (mt-10) REVERT: M 91 TYR cc_start: 0.9329 (p90) cc_final: 0.9097 (p90) REVERT: M 103 TYR cc_start: 0.9105 (m-80) cc_final: 0.8641 (m-80) REVERT: M 104 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8555 (mt-10) REVERT: M 127 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7953 (tttm) REVERT: N 32 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8318 (mm-30) REVERT: O 13 ARG cc_start: 0.8580 (tmm160) cc_final: 0.7999 (ttt90) REVERT: O 16 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7463 (mmt90) REVERT: O 80 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7572 (mt-10) REVERT: P 83 SER cc_start: 0.8458 (t) cc_final: 0.7860 (m) REVERT: Q 13 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8030 (mtp180) REVERT: R 19 THR cc_start: 0.8903 (m) cc_final: 0.8478 (t) REVERT: R 70 GLU cc_start: 0.8494 (tt0) cc_final: 0.8229 (tp30) REVERT: R 86 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: S 38 TYR cc_start: 0.8976 (m-80) cc_final: 0.8458 (m-80) REVERT: S 73 LYS cc_start: 0.8503 (mttt) cc_final: 0.8096 (mtpp) REVERT: T 33 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7767 (tttm) REVERT: U 47 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8023 (ttmm) REVERT: V 7 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: W 68 LYS cc_start: 0.8676 (tptp) cc_final: 0.8215 (tppt) REVERT: Y 2 LYS cc_start: 0.6799 (mtpt) cc_final: 0.6541 (tttm) REVERT: Y 6 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7664 (mt) REVERT: Y 23 ARG cc_start: 0.8334 (mtm180) cc_final: 0.7925 (mtt90) REVERT: Z 56 LYS cc_start: 0.8269 (pttt) cc_final: 0.7891 (pttp) REVERT: Z 58 GLU cc_start: 0.7413 (tt0) cc_final: 0.6899 (tt0) REVERT: b 40 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.6988 (mmt180) REVERT: d 14 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8401 (mtt-85) REVERT: f 8 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8564 (mtpt) REVERT: g 37 LYS cc_start: 0.7139 (tptt) cc_final: 0.6715 (mmtt) REVERT: g 63 ARG cc_start: 0.7404 (ttp-110) cc_final: 0.7123 (ttp80) REVERT: g 105 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7418 (tttm) REVERT: g 110 SER cc_start: 0.7608 (OUTLIER) cc_final: 0.7000 (m) REVERT: g 137 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5958 (tpp80) REVERT: g 138 THR cc_start: 0.6839 (m) cc_final: 0.6491 (p) REVERT: g 146 ASN cc_start: 0.7222 (m-40) cc_final: 0.6217 (t0) REVERT: h 85 GLU cc_start: 0.7430 (tp30) cc_final: 0.6958 (mm-30) REVERT: h 89 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7321 (ptpp) REVERT: h 110 GLU cc_start: 0.7696 (mp0) cc_final: 0.7461 (mp0) REVERT: h 121 THR cc_start: 0.8890 (m) cc_final: 0.8327 (m) REVERT: h 147 LYS cc_start: 0.8803 (mmpt) cc_final: 0.8473 (mmmt) REVERT: h 164 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8579 (ptt-90) REVERT: h 187 SER cc_start: 0.8985 (t) cc_final: 0.8621 (t) REVERT: h 193 TYR cc_start: 0.8383 (m-80) cc_final: 0.8122 (m-10) REVERT: i 45 LYS cc_start: 0.7843 (mttm) cc_final: 0.7567 (mtpm) REVERT: i 70 ARG cc_start: 0.8717 (tpp80) cc_final: 0.7632 (ttp-110) REVERT: i 172 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7242 (tm-30) REVERT: i 187 GLU cc_start: 0.8023 (tt0) cc_final: 0.7589 (mm-30) REVERT: j 13 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: j 26 LYS cc_start: 0.9104 (ttpm) cc_final: 0.8746 (ttmm) REVERT: j 115 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8265 (mt) REVERT: k 7 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8655 (t) REVERT: l 21 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: l 52 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: l 58 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: l 78 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.5754 (tmt-80) REVERT: l 79 ARG cc_start: 0.5723 (OUTLIER) cc_final: 0.5124 (tmt170) REVERT: l 129 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7384 (mm-30) REVERT: l 130 ASN cc_start: 0.8130 (t0) cc_final: 0.7894 (t0) REVERT: m 4 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8704 (mp10) REVERT: m 31 LYS cc_start: 0.8458 (ttpp) cc_final: 0.8204 (ptmm) REVERT: m 43 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: m 50 LYS cc_start: 0.8141 (tttp) cc_final: 0.7570 (tptm) REVERT: m 58 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8115 (mt-10) REVERT: m 74 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8418 (p) REVERT: m 118 GLN cc_start: 0.7718 (tt0) cc_final: 0.7457 (mt0) REVERT: n 22 LYS cc_start: 0.7432 (tttt) cc_final: 0.6996 (mttm) REVERT: n 33 ARG cc_start: 0.7607 (mtt90) cc_final: 0.7180 (mtm180) REVERT: n 42 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7425 (mm-30) REVERT: n 64 TYR cc_start: 0.8799 (t80) cc_final: 0.8594 (t80) REVERT: n 124 ARG cc_start: 0.8744 (ttm-80) cc_final: 0.8427 (mtm-85) REVERT: o 7 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6875 (mmm160) REVERT: o 60 ASP cc_start: 0.8726 (m-30) cc_final: 0.8442 (m-30) REVERT: p 18 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: p 69 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7188 (mmm160) REVERT: p 76 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: p 119 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7411 (t0) REVERT: q 9 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7853 (ttm110) REVERT: q 15 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5771 (mtpp) REVERT: q 25 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8196 (mm-30) REVERT: q 44 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8403 (tppp) REVERT: q 108 LYS cc_start: 0.8606 (mttt) cc_final: 0.8147 (mmtm) REVERT: r 29 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7412 (mtt180) REVERT: r 76 SER cc_start: 0.8110 (m) cc_final: 0.7736 (p) REVERT: s 40 ASP cc_start: 0.7796 (m-30) cc_final: 0.7554 (m-30) REVERT: t 83 GLU cc_start: 0.8372 (tt0) cc_final: 0.8040 (tt0) REVERT: u 42 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8477 (mp) REVERT: u 51 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.7785 (ttp80) REVERT: u 63 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: w 35 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: w 48 ARG cc_start: 0.7807 (mtm110) cc_final: 0.6681 (mmt90) REVERT: x 17 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7620 (mmpt) REVERT: x 32 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7733 (ptp-170) REVERT: x 63 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7734 (p) REVERT: y 48 GLN cc_start: 0.8050 (mm110) cc_final: 0.7687 (mm-40) REVERT: y 49 LYS cc_start: 0.8211 (tppt) cc_final: 0.7686 (ttmm) REVERT: y 85 LYS cc_start: 0.7383 (tttt) cc_final: 0.6887 (mmmm) REVERT: z 31 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: z 33 ARG cc_start: 0.8032 (tmt170) cc_final: 0.7494 (ttm170) REVERT: z 55 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.6697 (mmt180) outliers start: 338 outliers final: 212 residues processed: 1194 average time/residue: 2.2779 time to fit residues: 3887.9343 Evaluate side-chains 1263 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 984 time to evaluate : 6.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain 7 residue 133 GLN Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 240 ARG Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 268 THR Chi-restraints excluded: chain 7 residue 297 GLU Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain 7 residue 360 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 45 LYS Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 153 ASP Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 182 ILE Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 52 GLN Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 4 GLN Chi-restraints excluded: chain m residue 43 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 15 LYS Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 75 GLN Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 11 ASP Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 29 ARG Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain u residue 63 GLN Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 31 GLU Chi-restraints excluded: chain z residue 44 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 942 optimal weight: 0.9990 chunk 992 optimal weight: 6.9990 chunk 905 optimal weight: 3.9990 chunk 965 optimal weight: 4.9990 chunk 581 optimal weight: 8.9990 chunk 420 optimal weight: 7.9990 chunk 758 optimal weight: 0.9990 chunk 296 optimal weight: 8.9990 chunk 872 optimal weight: 6.9990 chunk 913 optimal weight: 1.9990 chunk 962 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 304 ASN 7 313 ASN E 23 ASN E 63 GLN F 104 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 93 ASN N 18 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN Q 72 ASN Y 27 ASN e 28 ASN h 102 ASN ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 28 ASN u 18 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 84 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 162068 Z= 0.201 Angle : 0.622 15.762 241755 Z= 0.335 Chirality : 0.035 0.395 30685 Planarity : 0.006 0.129 13434 Dihedral : 23.249 179.765 79446 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 5.41 % Allowed : 24.59 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.11), residues: 6269 helix: 1.80 (0.11), residues: 2271 sheet: -0.83 (0.14), residues: 1202 loop : -0.71 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 248 HIS 0.010 0.001 HIS w 74 PHE 0.020 0.001 PHE G 91 TYR 0.025 0.002 TYR h 42 ARG 0.014 0.000 ARG M 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1004 time to evaluate : 6.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 30 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: 6 31 LYS cc_start: 0.9051 (tptp) cc_final: 0.8820 (tmtm) REVERT: 6 33 LYS cc_start: 0.9170 (mptp) cc_final: 0.8870 (mmtm) REVERT: 7 133 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: 7 157 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6718 (tp30) REVERT: 7 172 GLU cc_start: 0.7524 (tt0) cc_final: 0.6898 (tp30) REVERT: 7 182 LYS cc_start: 0.7345 (tttt) cc_final: 0.7027 (mtpt) REVERT: 7 200 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7214 (ttm-80) REVERT: 7 234 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6182 (tp) REVERT: 7 255 ASN cc_start: 0.8055 (m-40) cc_final: 0.7717 (m-40) REVERT: 7 256 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7957 (ptm160) REVERT: 7 292 LYS cc_start: 0.7665 (ttmp) cc_final: 0.7059 (tmtm) REVERT: 7 297 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: 7 303 LYS cc_start: 0.6973 (mttm) cc_final: 0.6604 (mptt) REVERT: 7 310 MET cc_start: 0.7327 (mmp) cc_final: 0.6667 (mmm) REVERT: 7 329 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: 7 352 SER cc_start: 0.8588 (t) cc_final: 0.8304 (t) REVERT: B 23 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: B 97 LYS cc_start: 0.8421 (mptt) cc_final: 0.7770 (ttpt) REVERT: B 115 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8033 (tp40) REVERT: B 133 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7419 (ptp90) REVERT: B 145 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8270 (mt-10) REVERT: B 161 TYR cc_start: 0.9014 (p90) cc_final: 0.8785 (p90) REVERT: B 188 CYS cc_start: 0.8815 (m) cc_final: 0.8443 (m) REVERT: B 242 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8492 (mptt) REVERT: B 251 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8660 (mm-40) REVERT: B 270 ARG cc_start: 0.8049 (mmm160) cc_final: 0.6827 (ttt-90) REVERT: C 7 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8286 (ttpp) REVERT: C 28 GLU cc_start: 0.8333 (tt0) cc_final: 0.7967 (tt0) REVERT: C 30 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7912 (tp30) REVERT: C 33 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7820 (ptt90) REVERT: C 105 LYS cc_start: 0.8449 (mttt) cc_final: 0.7968 (mmtt) REVERT: C 165 MET cc_start: 0.8777 (ttt) cc_final: 0.8436 (ttt) REVERT: C 176 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: D 21 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7324 (ptm-80) REVERT: D 69 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7110 (ptp-170) REVERT: D 88 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7806 (mmp80) REVERT: D 122 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: D 132 LYS cc_start: 0.7577 (tttm) cc_final: 0.7234 (ttpt) REVERT: D 136 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6961 (tm130) REVERT: D 139 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7660 (tttp) REVERT: D 155 GLU cc_start: 0.7844 (tp30) cc_final: 0.7396 (mp0) REVERT: D 171 ASP cc_start: 0.8197 (t70) cc_final: 0.7759 (m-30) REVERT: D 197 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7394 (tp30) REVERT: E 19 GLU cc_start: 0.8561 (tt0) cc_final: 0.8319 (tp30) REVERT: E 32 GLU cc_start: 0.7904 (tt0) cc_final: 0.7550 (tt0) REVERT: E 115 ARG cc_start: 0.7436 (mmm160) cc_final: 0.7105 (mmm160) REVERT: E 120 LYS cc_start: 0.8739 (mttt) cc_final: 0.8292 (ptmt) REVERT: E 165 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7582 (mt-10) REVERT: F 27 LYS cc_start: 0.7009 (mttt) cc_final: 0.6429 (mppt) REVERT: F 95 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7901 (ptm-80) REVERT: F 99 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7790 (mtmm) REVERT: F 176 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5347 (ptpt) REVERT: G 11 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7209 (m110) REVERT: G 35 LYS cc_start: 0.7733 (mttt) cc_final: 0.7485 (mttp) REVERT: G 66 ASN cc_start: 0.4398 (OUTLIER) cc_final: 0.3986 (p0) REVERT: G 114 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6797 (mm-30) REVERT: G 117 LEU cc_start: 0.5371 (mt) cc_final: 0.4878 (OUTLIER) REVERT: G 127 GLU cc_start: 0.5463 (pt0) cc_final: 0.5056 (mp0) REVERT: H 38 MET cc_start: 0.2437 (mtm) cc_final: 0.1920 (mmm) REVERT: J 35 ARG cc_start: 0.8728 (mtt90) cc_final: 0.8441 (mtp85) REVERT: J 98 GLU cc_start: 0.8719 (mp0) cc_final: 0.8364 (mp0) REVERT: J 108 MET cc_start: 0.8952 (mtt) cc_final: 0.8577 (mtt) REVERT: K 93 GLN cc_start: 0.8382 (pt0) cc_final: 0.7690 (mm110) REVERT: K 113 MET cc_start: 0.8031 (tpt) cc_final: 0.7774 (mmm) REVERT: K 114 LYS cc_start: 0.8394 (tttt) cc_final: 0.7870 (mmpt) REVERT: M 6 ARG cc_start: 0.7837 (mtp-110) cc_final: 0.7093 (mtm-85) REVERT: M 60 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: M 75 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8174 (mt-10) REVERT: M 104 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: M 127 LYS cc_start: 0.8331 (ttmp) cc_final: 0.7942 (tptm) REVERT: N 32 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8300 (mm-30) REVERT: O 13 ARG cc_start: 0.8554 (tmm160) cc_final: 0.7977 (ttt90) REVERT: O 16 ARG cc_start: 0.8330 (mmm160) cc_final: 0.7570 (mmt90) REVERT: P 7 GLN cc_start: 0.7914 (tp40) cc_final: 0.7650 (tp40) REVERT: P 83 SER cc_start: 0.8408 (t) cc_final: 0.7793 (m) REVERT: Q 13 ARG cc_start: 0.8227 (ttt90) cc_final: 0.7897 (mtp180) REVERT: R 19 THR cc_start: 0.8890 (m) cc_final: 0.8462 (t) REVERT: R 70 GLU cc_start: 0.8480 (tt0) cc_final: 0.8234 (tp30) REVERT: R 86 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8562 (mt0) REVERT: S 38 TYR cc_start: 0.8902 (m-80) cc_final: 0.8499 (m-80) REVERT: S 73 LYS cc_start: 0.8449 (mttt) cc_final: 0.8003 (mtpp) REVERT: T 1 MET cc_start: 0.4360 (tpp) cc_final: 0.4026 (mtm) REVERT: T 24 MET cc_start: 0.7817 (ttm) cc_final: 0.7468 (tpt) REVERT: T 33 LYS cc_start: 0.7994 (ttmm) cc_final: 0.7660 (tttp) REVERT: U 47 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8024 (ttmm) REVERT: V 7 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: V 43 ASP cc_start: 0.8279 (t0) cc_final: 0.7989 (t0) REVERT: W 68 LYS cc_start: 0.8691 (tptp) cc_final: 0.8233 (tppt) REVERT: Y 6 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7609 (mt) REVERT: Y 23 ARG cc_start: 0.8316 (mtm180) cc_final: 0.7899 (mtt90) REVERT: Z 4 THR cc_start: 0.8033 (m) cc_final: 0.7778 (p) REVERT: Z 56 LYS cc_start: 0.8236 (pttt) cc_final: 0.7856 (pttp) REVERT: Z 58 GLU cc_start: 0.7326 (tt0) cc_final: 0.6815 (tt0) REVERT: b 40 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.6870 (mmt180) REVERT: d 14 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8298 (mtt-85) REVERT: e 15 LYS cc_start: 0.8617 (mptt) cc_final: 0.8399 (mppt) REVERT: f 8 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8560 (mtpt) REVERT: g 37 LYS cc_start: 0.7138 (tptt) cc_final: 0.6687 (mmtt) REVERT: g 63 ARG cc_start: 0.7445 (ttp-110) cc_final: 0.7134 (ttp80) REVERT: g 105 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7286 (tttm) REVERT: g 137 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.6004 (tpp80) REVERT: g 138 THR cc_start: 0.6834 (m) cc_final: 0.6481 (p) REVERT: g 146 ASN cc_start: 0.7232 (m-40) cc_final: 0.6219 (OUTLIER) REVERT: h 85 GLU cc_start: 0.7475 (tp30) cc_final: 0.7077 (mm-30) REVERT: h 89 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7315 (ptpp) REVERT: h 110 GLU cc_start: 0.7709 (mp0) cc_final: 0.7451 (mp0) REVERT: h 121 THR cc_start: 0.8873 (m) cc_final: 0.8475 (m) REVERT: h 187 SER cc_start: 0.8931 (t) cc_final: 0.8541 (t) REVERT: h 193 TYR cc_start: 0.8341 (m-80) cc_final: 0.8100 (m-10) REVERT: h 200 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8685 (t) REVERT: i 45 LYS cc_start: 0.7829 (mttm) cc_final: 0.7552 (mtpm) REVERT: i 70 ARG cc_start: 0.8699 (tpp80) cc_final: 0.7590 (ttp-110) REVERT: i 172 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7242 (tm-30) REVERT: i 187 GLU cc_start: 0.8034 (tt0) cc_final: 0.7621 (mm-30) REVERT: j 26 LYS cc_start: 0.9077 (ttpm) cc_final: 0.8695 (ttmm) REVERT: j 115 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8182 (mt) REVERT: k 7 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8686 (t) REVERT: l 21 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: l 52 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: l 78 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.5685 (tmt-80) REVERT: l 79 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.5093 (tmt-80) REVERT: l 129 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7371 (mm-30) REVERT: l 130 ASN cc_start: 0.8139 (t0) cc_final: 0.7914 (t0) REVERT: m 4 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: m 31 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8179 (ptmm) REVERT: m 43 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: m 50 LYS cc_start: 0.8119 (tttp) cc_final: 0.7554 (tptm) REVERT: m 51 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8099 (t) REVERT: m 58 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8122 (mt-10) REVERT: m 74 SER cc_start: 0.8772 (p) cc_final: 0.8419 (p) REVERT: m 118 GLN cc_start: 0.7707 (tt0) cc_final: 0.7393 (mt0) REVERT: n 22 LYS cc_start: 0.7467 (tttt) cc_final: 0.7044 (mttm) REVERT: n 33 ARG cc_start: 0.7567 (mtt90) cc_final: 0.7234 (mtp180) REVERT: n 42 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7409 (mm-30) REVERT: n 64 TYR cc_start: 0.8782 (t80) cc_final: 0.8528 (t80) REVERT: o 7 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6852 (mmm160) REVERT: o 60 ASP cc_start: 0.8726 (m-30) cc_final: 0.8424 (m-30) REVERT: p 18 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: p 69 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7215 (mmm160) REVERT: p 76 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: q 9 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7810 (ttm170) REVERT: q 25 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8165 (mm-30) REVERT: q 44 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8412 (tppp) REVERT: q 108 LYS cc_start: 0.8598 (mttt) cc_final: 0.8138 (mmtm) REVERT: r 29 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7350 (mtt180) REVERT: r 76 SER cc_start: 0.8054 (m) cc_final: 0.7709 (p) REVERT: r 81 MET cc_start: 0.8150 (mtt) cc_final: 0.7880 (mtt) REVERT: r 93 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7947 (mmp80) REVERT: s 40 ASP cc_start: 0.7776 (m-30) cc_final: 0.7532 (m-30) REVERT: t 40 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: t 83 GLU cc_start: 0.8385 (tt0) cc_final: 0.8060 (tt0) REVERT: u 42 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8477 (mp) REVERT: w 35 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: x 17 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7626 (mmpt) REVERT: x 32 ARG cc_start: 0.8172 (ptt180) cc_final: 0.7751 (ptp-170) REVERT: x 63 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7645 (p) REVERT: y 48 GLN cc_start: 0.8000 (mm110) cc_final: 0.7725 (tp40) REVERT: y 49 LYS cc_start: 0.8184 (tppt) cc_final: 0.7664 (ttmm) REVERT: y 85 LYS cc_start: 0.7309 (tttt) cc_final: 0.6795 (mmmm) REVERT: z 31 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: z 33 ARG cc_start: 0.8035 (tmt170) cc_final: 0.7497 (ttm170) REVERT: z 55 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.6721 (mmt180) outliers start: 282 outliers final: 183 residues processed: 1177 average time/residue: 2.2751 time to fit residues: 3823.6363 Evaluate side-chains 1228 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 989 time to evaluate : 6.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain 6 residue 42 LYS Chi-restraints excluded: chain 7 residue 133 GLN Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 240 ARG Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 268 THR Chi-restraints excluded: chain 7 residue 297 GLU Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 45 LYS Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 153 ASP Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 72 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 173 VAL Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 52 GLN Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 4 GLN Chi-restraints excluded: chain m residue 43 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 75 GLN Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 29 ARG Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain u residue 63 GLN Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 31 GLU Chi-restraints excluded: chain z residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 634 optimal weight: 0.0670 chunk 1020 optimal weight: 1.9990 chunk 623 optimal weight: 0.6980 chunk 484 optimal weight: 0.7980 chunk 709 optimal weight: 7.9990 chunk 1070 optimal weight: 7.9990 chunk 985 optimal weight: 2.9990 chunk 852 optimal weight: 0.0670 chunk 88 optimal weight: 30.0000 chunk 658 optimal weight: 8.9990 chunk 522 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 ASN E 63 GLN F 104 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 6 GLN Y 27 ASN e 28 ASN h 102 ASN ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 28 ASN u 18 GLN w 74 HIS y 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.157 162068 Z= 0.135 Angle : 0.602 15.559 241755 Z= 0.327 Chirality : 0.034 0.869 30685 Planarity : 0.006 0.125 13434 Dihedral : 23.266 179.770 79437 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 4.27 % Allowed : 25.84 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.11), residues: 6269 helix: 1.92 (0.11), residues: 2278 sheet: -0.72 (0.14), residues: 1195 loop : -0.64 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 248 HIS 0.010 0.001 HIS w 74 PHE 0.021 0.001 PHE G 91 TYR 0.033 0.002 TYR R 2 ARG 0.016 0.001 ARG M 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1010 time to evaluate : 6.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 30 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: 6 31 LYS cc_start: 0.9010 (tptp) cc_final: 0.8789 (tmtm) REVERT: 6 33 LYS cc_start: 0.9154 (mptp) cc_final: 0.8860 (mmtt) REVERT: 7 114 GLU cc_start: 0.7034 (pt0) cc_final: 0.6615 (pp20) REVERT: 7 125 SER cc_start: 0.9048 (t) cc_final: 0.8777 (m) REVERT: 7 133 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: 7 157 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6751 (tp30) REVERT: 7 172 GLU cc_start: 0.7497 (tt0) cc_final: 0.6895 (tp30) REVERT: 7 182 LYS cc_start: 0.7186 (tttt) cc_final: 0.6896 (mtpt) REVERT: 7 234 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6192 (tp) REVERT: 7 255 ASN cc_start: 0.8077 (m-40) cc_final: 0.7763 (m-40) REVERT: 7 256 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7813 (ptm160) REVERT: 7 292 LYS cc_start: 0.7643 (ttmp) cc_final: 0.7051 (tttm) REVERT: 7 297 GLU cc_start: 0.7230 (tp30) cc_final: 0.6794 (tm-30) REVERT: 7 303 LYS cc_start: 0.6969 (mttm) cc_final: 0.6599 (mptt) REVERT: 7 310 MET cc_start: 0.7318 (mmp) cc_final: 0.6691 (mmm) REVERT: 7 329 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: B 23 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: B 97 LYS cc_start: 0.8424 (mptt) cc_final: 0.7785 (ttpt) REVERT: B 125 LYS cc_start: 0.8497 (ptmm) cc_final: 0.8053 (pttm) REVERT: B 133 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7388 (ptp90) REVERT: B 161 TYR cc_start: 0.8978 (p90) cc_final: 0.8708 (p90) REVERT: B 188 CYS cc_start: 0.8719 (m) cc_final: 0.8278 (m) REVERT: B 242 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8448 (mptt) REVERT: B 251 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8642 (mm-40) REVERT: B 270 ARG cc_start: 0.8002 (mmm160) cc_final: 0.6788 (ttt-90) REVERT: C 7 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8252 (ttpp) REVERT: C 28 GLU cc_start: 0.8300 (tt0) cc_final: 0.7954 (tt0) REVERT: C 30 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7895 (tp30) REVERT: C 33 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7813 (ptt90) REVERT: C 105 LYS cc_start: 0.8437 (mttt) cc_final: 0.7957 (mmtt) REVERT: C 165 MET cc_start: 0.8755 (ttt) cc_final: 0.8417 (ttt) REVERT: C 176 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: D 21 ARG cc_start: 0.7635 (ptm160) cc_final: 0.7337 (ptm-80) REVERT: D 88 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7779 (mmp80) REVERT: D 122 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: D 132 LYS cc_start: 0.7468 (tttm) cc_final: 0.7140 (ttpt) REVERT: D 136 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: D 139 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7608 (tttp) REVERT: D 155 GLU cc_start: 0.7820 (tp30) cc_final: 0.7381 (mp0) REVERT: D 171 ASP cc_start: 0.8186 (t70) cc_final: 0.7831 (t70) REVERT: D 197 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7367 (tp30) REVERT: E 19 GLU cc_start: 0.8536 (tt0) cc_final: 0.8314 (tp30) REVERT: E 32 GLU cc_start: 0.7935 (tt0) cc_final: 0.7619 (tt0) REVERT: E 115 ARG cc_start: 0.7472 (mmm160) cc_final: 0.7133 (mmm160) REVERT: E 120 LYS cc_start: 0.8719 (mttt) cc_final: 0.8274 (ptmt) REVERT: F 27 LYS cc_start: 0.6925 (mttt) cc_final: 0.6412 (mppt) REVERT: F 95 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7832 (ptm-80) REVERT: F 99 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7775 (mtmm) REVERT: F 176 LYS cc_start: 0.6136 (OUTLIER) cc_final: 0.5329 (ptpt) REVERT: G 11 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7241 (m110) REVERT: G 35 LYS cc_start: 0.7728 (mttt) cc_final: 0.7462 (mttp) REVERT: G 60 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7054 (mm-30) REVERT: G 66 ASN cc_start: 0.4387 (OUTLIER) cc_final: 0.3960 (p0) REVERT: G 114 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6796 (mm-30) REVERT: G 117 LEU cc_start: 0.5388 (mt) cc_final: 0.4912 (OUTLIER) REVERT: G 127 GLU cc_start: 0.5489 (pt0) cc_final: 0.5087 (mp0) REVERT: H 38 MET cc_start: 0.2429 (mtm) cc_final: 0.1917 (mmm) REVERT: I 116 MET cc_start: 0.2000 (mmp) cc_final: 0.1682 (tmm) REVERT: J 35 ARG cc_start: 0.8706 (mtt90) cc_final: 0.8413 (mtp85) REVERT: J 98 GLU cc_start: 0.8733 (mp0) cc_final: 0.8378 (mp0) REVERT: J 108 MET cc_start: 0.8902 (mtt) cc_final: 0.8531 (mtt) REVERT: K 93 GLN cc_start: 0.8309 (pt0) cc_final: 0.7754 (mm110) REVERT: K 113 MET cc_start: 0.7948 (tpt) cc_final: 0.7701 (mmm) REVERT: K 114 LYS cc_start: 0.8385 (tttt) cc_final: 0.7792 (mmpt) REVERT: M 6 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7177 (mtm-85) REVERT: M 60 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: M 75 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8162 (mt-10) REVERT: M 104 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: M 127 LYS cc_start: 0.8341 (ttmp) cc_final: 0.7951 (tptm) REVERT: N 32 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8334 (mm-30) REVERT: O 13 ARG cc_start: 0.8530 (tmm160) cc_final: 0.7953 (ttt90) REVERT: O 16 ARG cc_start: 0.8330 (mmm160) cc_final: 0.7492 (mmt90) REVERT: O 80 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7674 (mp0) REVERT: P 7 GLN cc_start: 0.7925 (tp40) cc_final: 0.7667 (tp40) REVERT: P 83 SER cc_start: 0.8354 (t) cc_final: 0.7744 (m) REVERT: Q 13 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7858 (mtp180) REVERT: R 70 GLU cc_start: 0.8483 (tt0) cc_final: 0.8248 (tp30) REVERT: R 86 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8514 (mt0) REVERT: S 38 TYR cc_start: 0.8793 (m-80) cc_final: 0.8422 (m-80) REVERT: S 73 LYS cc_start: 0.8428 (mttt) cc_final: 0.8010 (mtpp) REVERT: T 24 MET cc_start: 0.7800 (ttm) cc_final: 0.7461 (tpt) REVERT: T 33 LYS cc_start: 0.8004 (ttmm) cc_final: 0.7675 (tttp) REVERT: V 43 ASP cc_start: 0.8239 (t0) cc_final: 0.7953 (t0) REVERT: W 68 LYS cc_start: 0.8680 (tptp) cc_final: 0.8254 (tppt) REVERT: X 74 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7585 (mtp180) REVERT: Y 6 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7622 (mt) REVERT: Y 23 ARG cc_start: 0.8312 (mtm180) cc_final: 0.7909 (mtt90) REVERT: Z 6 LYS cc_start: 0.7761 (mptp) cc_final: 0.7344 (mmtm) REVERT: Z 37 GLU cc_start: 0.8514 (tp30) cc_final: 0.7760 (tt0) REVERT: Z 56 LYS cc_start: 0.8180 (pttt) cc_final: 0.7789 (pttp) REVERT: Z 58 GLU cc_start: 0.7280 (tt0) cc_final: 0.6777 (tt0) REVERT: c 33 LYS cc_start: 0.7850 (mptm) cc_final: 0.7310 (mtmt) REVERT: d 14 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8240 (mtt-85) REVERT: e 15 LYS cc_start: 0.8601 (mptt) cc_final: 0.8335 (mppt) REVERT: e 30 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8152 (mpt90) REVERT: f 8 LYS cc_start: 0.8878 (mttm) cc_final: 0.8558 (mtpt) REVERT: g 37 LYS cc_start: 0.7132 (tptt) cc_final: 0.6703 (mmpt) REVERT: g 63 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.7145 (ttp80) REVERT: g 105 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7250 (tttm) REVERT: g 110 SER cc_start: 0.7603 (OUTLIER) cc_final: 0.7030 (m) REVERT: g 137 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.6012 (tpp80) REVERT: g 138 THR cc_start: 0.6827 (m) cc_final: 0.6479 (p) REVERT: h 82 GLU cc_start: 0.5535 (tm-30) cc_final: 0.5211 (pp20) REVERT: h 85 GLU cc_start: 0.7497 (tp30) cc_final: 0.7077 (mm-30) REVERT: h 89 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7276 (ptpp) REVERT: h 110 GLU cc_start: 0.7819 (mp0) cc_final: 0.7553 (mp0) REVERT: h 187 SER cc_start: 0.8881 (t) cc_final: 0.8504 (t) REVERT: h 193 TYR cc_start: 0.8340 (m-80) cc_final: 0.8113 (m-10) REVERT: i 45 LYS cc_start: 0.7849 (mttm) cc_final: 0.7535 (mtpm) REVERT: i 59 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8747 (mm-40) REVERT: i 70 ARG cc_start: 0.8646 (tpp80) cc_final: 0.7556 (ttp-110) REVERT: i 172 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7286 (tm-30) REVERT: i 187 GLU cc_start: 0.8061 (tt0) cc_final: 0.7644 (mm-30) REVERT: j 26 LYS cc_start: 0.9056 (ttpm) cc_final: 0.8678 (ttmm) REVERT: j 45 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7641 (mtp180) REVERT: j 96 MET cc_start: 0.8970 (ptm) cc_final: 0.8565 (mtm) REVERT: j 111 MET cc_start: 0.8872 (ttt) cc_final: 0.8654 (mtt) REVERT: j 115 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8218 (mt) REVERT: l 21 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: l 52 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: l 78 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.5759 (tmt-80) REVERT: l 79 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.4955 (tmt-80) REVERT: l 111 ARG cc_start: 0.7388 (mmm160) cc_final: 0.7174 (mmm160) REVERT: l 129 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7410 (mm-30) REVERT: l 144 MET cc_start: 0.7180 (ttt) cc_final: 0.6963 (ttt) REVERT: m 43 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: m 50 LYS cc_start: 0.8107 (tttp) cc_final: 0.7553 (tptm) REVERT: m 51 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8252 (t) REVERT: m 58 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8096 (mt-10) REVERT: m 74 SER cc_start: 0.8765 (p) cc_final: 0.8436 (p) REVERT: m 118 GLN cc_start: 0.7725 (tt0) cc_final: 0.7412 (mt0) REVERT: n 22 LYS cc_start: 0.7500 (tttt) cc_final: 0.7077 (mttm) REVERT: n 33 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7135 (mtm180) REVERT: n 42 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7404 (mm-30) REVERT: o 7 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6839 (mmm160) REVERT: o 60 ASP cc_start: 0.8735 (m-30) cc_final: 0.8419 (m-30) REVERT: p 69 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7235 (mmm160) REVERT: p 76 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: q 9 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7859 (ttp-110) REVERT: q 25 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8185 (mm-30) REVERT: q 44 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8424 (tppp) REVERT: q 108 LYS cc_start: 0.8581 (mttt) cc_final: 0.8128 (mmtm) REVERT: r 29 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7062 (ttm170) REVERT: r 76 SER cc_start: 0.8008 (m) cc_final: 0.7655 (p) REVERT: r 81 MET cc_start: 0.8133 (mtt) cc_final: 0.7799 (mtt) REVERT: r 93 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7836 (mmp80) REVERT: s 49 GLN cc_start: 0.7849 (mt0) cc_final: 0.7645 (mt0) REVERT: t 40 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: t 83 GLU cc_start: 0.8382 (tt0) cc_final: 0.8057 (tt0) REVERT: u 42 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8451 (mp) REVERT: u 51 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.7932 (ttp80) REVERT: v 60 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: w 12 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6204 (mmm160) REVERT: x 17 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7512 (mmpt) REVERT: x 32 ARG cc_start: 0.8157 (ptt180) cc_final: 0.7745 (ptp-170) REVERT: x 63 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7654 (p) REVERT: y 49 LYS cc_start: 0.8232 (tppt) cc_final: 0.7811 (ttmm) REVERT: y 85 LYS cc_start: 0.7287 (tttt) cc_final: 0.6776 (mmmm) REVERT: z 33 ARG cc_start: 0.8044 (tmt170) cc_final: 0.7531 (ttm170) REVERT: z 55 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.6814 (mmt180) outliers start: 223 outliers final: 136 residues processed: 1152 average time/residue: 2.3906 time to fit residues: 3930.4397 Evaluate side-chains 1176 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 992 time to evaluate : 6.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain 6 residue 42 LYS Chi-restraints excluded: chain 7 residue 133 GLN Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 234 ILE Chi-restraints excluded: chain 7 residue 256 ARG Chi-restraints excluded: chain 7 residue 265 HIS Chi-restraints excluded: chain 7 residue 312 ASP Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 7 residue 331 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 31 ARG Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 34 LYS Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 45 LYS Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 153 ASP Chi-restraints excluded: chain g residue 210 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 110 THR Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 52 GLN Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 43 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 75 GLN Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 29 ARG Chi-restraints excluded: chain r residue 54 ASP Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain u residue 63 GLN Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 51 ASN Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 27 MET Chi-restraints excluded: chain z residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 677 optimal weight: 0.0980 chunk 908 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 786 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 854 optimal weight: 5.9990 chunk 357 optimal weight: 8.9990 chunk 877 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 ASN E 63 GLN F 104 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN N 18 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 6 GLN Y 27 ASN Z 9 GLN b 4 GLN e 28 ASN h 102 ASN ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN l 130 ASN n 126 GLN p 28 ASN v 9 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 84 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.101064 restraints weight = 182641.437| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 0.71 r_work: 0.2820 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 162068 Z= 0.224 Angle : 0.633 59.039 241755 Z= 0.346 Chirality : 0.037 0.744 30685 Planarity : 0.006 0.125 13434 Dihedral : 23.260 179.719 79432 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.91 % Rotamer: Outliers : 4.12 % Allowed : 26.07 % Favored : 69.81 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 6269 helix: 1.90 (0.11), residues: 2279 sheet: -0.71 (0.14), residues: 1193 loop : -0.65 (0.11), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 248 HIS 0.008 0.001 HIS w 74 PHE 0.021 0.001 PHE G 91 TYR 0.029 0.002 TYR h 42 ARG 0.011 0.000 ARG M 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54072.20 seconds wall clock time: 936 minutes 35.47 seconds (56195.47 seconds total)